6ZLF | pdb_00006zlf

Aerobic crystal structure of F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution under 125 bars of krypton

PDB DOI: https://doi.org/10.2210/pdb6ZLF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermococcus thermolithotrophicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-30 Released: 2020-11-25
Deposition Author(s): Engilberge, S., Wagner, T., Carpentier, P., Girard, E., Shima, S.
Funding Organization(s): French National Research Agency, Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Krypton-derivatization highlights O 2 -channeling in a four-electron reducing oxidase.

Engilberge, S., Wagner, T., Carpentier, P., Girard, E., Shima, S.

(2020) Chem Commun (Camb) 56: 10863-10866

PubMed: 32940290 Search on PubMed
DOI: https://doi.org/10.1039/d0cc04557h
Primary Citation of Related Structures:
6ZK8, 6ZLF

PubMed Abstract:
F420H2-oxidase (FprA) catalyses the four-electron reduction of O2 to 2H2O using the reduced form of F420 as electron donor. The hydrophobic O2-channel detected by Kr-derivatization and the concerted movement of a gating loop could contribute to prevent unwanted side-reaction between the catalytic intermediates and solvents, therefore preventing reactive oxygen species formation.

Organizational Affiliation

Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.

Macromolecule Content

Total Structure Weight: 381.52 kDa
Atom Count: 28,860
Modelled Residue Count: 3,267
Deposited Residue Count: 3,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420H2 oxidase (FprA)	A B [auth F] C [auth G] D [auth H] E [auth I] A, B [auth F], C [auth G], D [auth H], E [auth I], F [auth J], G [auth K], H [auth L]	410	Methanothermococcus thermolithotrophicus	Mutation(s): 0
UniProt
Find proteins for A0A452CSW8 (Methanothermococcus thermolithotrophicus) Explore A0A452CSW8 Go to UniProtKB: A0A452CSW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A452CSW8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain NA [auth G] SDF format, chain NB [auth I] SDF format, chain U [auth A] SDF format, chain VC [auth L] SDF format, chain XA [auth H] SDF format, chain ZB [auth J] SDF format, chain LC [auth K] MOL2 format, chain BA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain NB [auth I] MOL2 format, chain U [auth A] MOL2 format, chain VC [auth L] MOL2 format, chain XA [auth H] MOL2 format, chain ZB [auth J] MOL2 format, chain LC [auth K] mmCIF format, chain BA [auth F] mmCIF format, chain NA [auth G] mmCIF format, chain NB [auth I] mmCIF format, chain U [auth A] mmCIF format, chain VC [auth L] mmCIF format, chain XA [auth H] mmCIF format, chain ZB [auth J] mmCIF format, chain LC [auth K]	BA [auth F] LC [auth K] NA [auth G] NB [auth I] U [auth A] BA [auth F], LC [auth K], NA [auth G], NB [auth I], U [auth A], VC [auth L], XA [auth H], ZB [auth J]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth F] Focus chain LC [auth K] Focus chain NA [auth G] Focus chain NB [auth I] Focus chain U [auth A] Focus chain VC [auth L] Focus chain XA [auth H] Focus chain ZB [auth J] Interactions & Density Focus chain BA [auth F] Focus chain LC [auth K] Focus chain NA [auth G] Focus chain NB [auth I] Focus chain U [auth A] Focus chain VC [auth L] Focus chain XA [auth H] Focus chain ZB [auth J]
FEO Query on FEO Download Ideal Coordinates CCD File SDF format, chain BB [auth I] SDF format, chain CC [auth K] SDF format, chain EA [auth F] SDF format, chain GA [auth G] SDF format, chain OC [auth L] SDF format, chain PA [auth H] SDF format, chain QB [auth J] SDF format, chain J [auth A] MOL2 format, chain BB [auth I] MOL2 format, chain CC [auth K] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain OC [auth L] MOL2 format, chain PA [auth H] MOL2 format, chain QB [auth J] MOL2 format, chain J [auth A] mmCIF format, chain BB [auth I] mmCIF format, chain CC [auth K] mmCIF format, chain EA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain OC [auth L] mmCIF format, chain PA [auth H] mmCIF format, chain QB [auth J] mmCIF format, chain J [auth A]	BB [auth I] CC [auth K] EA [auth F] GA [auth G] J [auth A] BB [auth I], CC [auth K], EA [auth F], GA [auth G], J [auth A], OC [auth L], PA [auth H], QB [auth J]	MU-OXO-DIIRON Fe₂ O NPMYUMBHPJGBFA-UHFFFAOYSA-N		Interactions Focus chain BB [auth I] Focus chain CC [auth K] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain J [auth A] Focus chain OC [auth L] Focus chain PA [auth H] Focus chain QB [auth J] Interactions & Density Focus chain BB [auth I] Focus chain CC [auth K] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain J [auth A] Focus chain OC [auth L] Focus chain PA [auth H] Focus chain QB [auth J]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain BC [auth K] SDF format, chain CB [auth I] SDF format, chain DC [auth K] SDF format, chain FA [auth G] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain PC [auth L] SDF format, chain QA [auth H] SDF format, chain DA [auth F] SDF format, chain DB [auth I] SDF format, chain EB [auth I] SDF format, chain EC [auth K] SDF format, chain FB [auth I] SDF format, chain NC [auth L] SDF format, chain PB [auth J] SDF format, chain RB [auth J] SDF format, chain SB [auth J] SDF format, chain ZA [auth I] MOL2 format, chain AB [auth I] MOL2 format, chain BC [auth K] MOL2 format, chain CB [auth I] MOL2 format, chain DC [auth K] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain PC [auth L] MOL2 format, chain QA [auth H] MOL2 format, chain DA [auth F] MOL2 format, chain DB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain EC [auth K] MOL2 format, chain FB [auth I] MOL2 format, chain NC [auth L] MOL2 format, chain PB [auth J] MOL2 format, chain RB [auth J] MOL2 format, chain SB [auth J] MOL2 format, chain ZA [auth I] mmCIF format, chain AB [auth I] mmCIF format, chain BC [auth K] mmCIF format, chain CB [auth I] mmCIF format, chain DC [auth K] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain PC [auth L] mmCIF format, chain QA [auth H] mmCIF format, chain DA [auth F] mmCIF format, chain DB [auth I] mmCIF format, chain EB [auth I] mmCIF format, chain EC [auth K] mmCIF format, chain FB [auth I] mmCIF format, chain NC [auth L] mmCIF format, chain PB [auth J] mmCIF format, chain RB [auth J] mmCIF format, chain SB [auth J] mmCIF format, chain ZA [auth I]	AB [auth I] BC [auth K] CB [auth I] DA [auth F] DB [auth I] AB [auth I], BC [auth K], CB [auth I], DA [auth F], DB [auth I], DC [auth K], EB [auth I], EC [auth K], FA [auth G], FB [auth I], HA [auth G], I [auth A], K [auth A], L [auth A], M [auth A], NC [auth L], PB [auth J], PC [auth L], QA [auth H], RB [auth J], SB [auth J], ZA [auth I]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BC [auth K] Focus chain CB [auth I] Focus chain DA [auth F] Focus chain DB [auth I] Focus chain DC [auth K] Focus chain EB [auth I] Focus chain EC [auth K] Focus chain FA [auth G] Focus chain FB [auth I] Focus chain HA [auth G] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NC [auth L] Focus chain PB [auth J] Focus chain PC [auth L] Focus chain QA [auth H] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain ZA [auth I] Interactions & Density Focus chain AB [auth I] Focus chain BC [auth K] Focus chain CB [auth I] Focus chain DA [auth F] Focus chain DB [auth I] Focus chain DC [auth K] Focus chain EB [auth I] Focus chain EC [auth K] Focus chain FA [auth G] Focus chain FB [auth I] Focus chain HA [auth G] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NC [auth L] Focus chain PB [auth J] Focus chain PC [auth L] Focus chain QA [auth H] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain ZA [auth I]
KR Query on KR Download Ideal Coordinates CCD File SDF format, chain GC [auth K] SDF format, chain IB [auth I] SDF format, chain IC [auth K] SDF format, chain KA [auth G] SDF format, chain KB [auth I] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QC [auth L] SDF format, chain R [auth A] SDF format, chain RA [auth H] SDF format, chain S [auth A] SDF format, chain SA [auth H] SDF format, chain T [auth A] SDF format, chain UB [auth J] SDF format, chain VA [auth H] SDF format, chain VB [auth J] SDF format, chain W [auth F] SDF format, chain XB [auth J] SDF format, chain YB [auth J] SDF format, chain Z [auth F] SDF format, chain AA [auth F] SDF format, chain FC [auth K] SDF format, chain GB [auth I] SDF format, chain HB [auth I] SDF format, chain HC [auth K] SDF format, chain IA [auth G] SDF format, chain JA [auth G] SDF format, chain JB [auth I] SDF format, chain JC [auth K] SDF format, chain KC [auth K] SDF format, chain LB [auth I] SDF format, chain MB [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain RC [auth L] SDF format, chain SC [auth L] SDF format, chain TA [auth H] SDF format, chain TB [auth J] SDF format, chain TC [auth L] SDF format, chain UA [auth H] SDF format, chain UC [auth L] SDF format, chain WA [auth H] SDF format, chain WB [auth J] SDF format, chain X [auth F] SDF format, chain XC [auth L] SDF format, chain Y [auth F] MOL2 format, chain GC [auth K] MOL2 format, chain IB [auth I] MOL2 format, chain IC [auth K] MOL2 format, chain KA [auth G] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QC [auth L] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth A] MOL2 format, chain UB [auth J] MOL2 format, chain VA [auth H] MOL2 format, chain VB [auth J] MOL2 format, chain W [auth F] MOL2 format, chain XB [auth J] MOL2 format, chain YB [auth J] MOL2 format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain FC [auth K] MOL2 format, chain GB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain HC [auth K] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain JB [auth I] MOL2 format, chain JC [auth K] MOL2 format, chain KC [auth K] MOL2 format, chain LB [auth I] MOL2 format, chain MB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain RC [auth L] MOL2 format, chain SC [auth L] MOL2 format, chain TA [auth H] MOL2 format, chain TB [auth J] MOL2 format, chain TC [auth L] MOL2 format, chain UA [auth H] MOL2 format, chain UC [auth L] MOL2 format, chain WA [auth H] MOL2 format, chain WB [auth J] MOL2 format, chain X [auth F] MOL2 format, chain XC [auth L] MOL2 format, chain Y [auth F] mmCIF format, chain GC [auth K] mmCIF format, chain IB [auth I] mmCIF format, chain IC [auth K] mmCIF format, chain KA [auth G] mmCIF format, chain KB [auth I] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QC [auth L] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth A] mmCIF format, chain UB [auth J] mmCIF format, chain VA [auth H] mmCIF format, chain VB [auth J] mmCIF format, chain W [auth F] mmCIF format, chain XB [auth J] mmCIF format, chain YB [auth J] mmCIF format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain FC [auth K] mmCIF format, chain GB [auth I] mmCIF format, chain HB [auth I] mmCIF format, chain HC [auth K] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain JB [auth I] mmCIF format, chain JC [auth K] mmCIF format, chain KC [auth K] mmCIF format, chain LB [auth I] mmCIF format, chain MB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain RC [auth L] mmCIF format, chain SC [auth L] mmCIF format, chain TA [auth H] mmCIF format, chain TB [auth J] mmCIF format, chain TC [auth L] mmCIF format, chain UA [auth H] mmCIF format, chain UC [auth L] mmCIF format, chain WA [auth H] mmCIF format, chain WB [auth J] mmCIF format, chain X [auth F] mmCIF format, chain XC [auth L] mmCIF format, chain Y [auth F]	AA [auth F] FC [auth K] GB [auth I] GC [auth K] HB [auth I] AA [auth F], FC [auth K], GB [auth I], GC [auth K], HB [auth I], HC [auth K], IA [auth G], IB [auth I], IC [auth K], JA [auth G], JB [auth I], JC [auth K], KA [auth G], KB [auth I], KC [auth K], LA [auth G], LB [auth I], MA [auth G], MB [auth I], N [auth A], O [auth A], P [auth A], Q [auth A], QC [auth L], R [auth A], RA [auth H], RC [auth L], S [auth A], SA [auth H], SC [auth L], T [auth A], TA [auth H], TB [auth J], TC [auth L], UA [auth H], UB [auth J], UC [auth L], VA [auth H], VB [auth J], W [auth F], WA [auth H], WB [auth J], X [auth F], XB [auth J], XC [auth L], Y [auth F], YB [auth J], Z [auth F]	KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain FC [auth K] Focus chain GB [auth I] Focus chain GC [auth K] Focus chain HB [auth I] Focus chain HC [auth K] Focus chain IA [auth G] Focus chain IB [auth I] Focus chain IC [auth K] Focus chain JA [auth G] Focus chain JB [auth I] Focus chain JC [auth K] Focus chain KA [auth G] Focus chain KB [auth I] Focus chain KC [auth K] Focus chain LA [auth G] Focus chain LB [auth I] Focus chain MA [auth G] Focus chain MB [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QC [auth L] Focus chain R [auth A] Focus chain RA [auth H] Focus chain RC [auth L] Focus chain S [auth A] Focus chain SA [auth H] Focus chain SC [auth L] Focus chain T [auth A] Focus chain TA [auth H] Focus chain TB [auth J] Focus chain TC [auth L] Focus chain UA [auth H] Focus chain UB [auth J] Focus chain UC [auth L] Focus chain VA [auth H] Focus chain VB [auth J] Focus chain W [auth F] Focus chain WA [auth H] Focus chain WB [auth J] Focus chain X [auth F] Focus chain XB [auth J] Focus chain XC [auth L] Focus chain Y [auth F] Focus chain YB [auth J] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain FC [auth K] Focus chain GB [auth I] Focus chain GC [auth K] Focus chain HB [auth I] Focus chain HC [auth K] Focus chain IA [auth G] Focus chain IB [auth I] Focus chain IC [auth K] Focus chain JA [auth G] Focus chain JB [auth I] Focus chain JC [auth K] Focus chain KA [auth G] Focus chain KB [auth I] Focus chain KC [auth K] Focus chain LA [auth G] Focus chain LB [auth I] Focus chain MA [auth G] Focus chain MB [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QC [auth L] Focus chain R [auth A] Focus chain RA [auth H] Focus chain RC [auth L] Focus chain S [auth A] Focus chain SA [auth H] Focus chain SC [auth L] Focus chain T [auth A] Focus chain TA [auth H] Focus chain TB [auth J] Focus chain TC [auth L] Focus chain UA [auth H] Focus chain UB [auth J] Focus chain UC [auth L] Focus chain VA [auth H] Focus chain VB [auth J] Focus chain W [auth F] Focus chain WA [auth H] Focus chain WB [auth J] Focus chain X [auth F] Focus chain XB [auth J] Focus chain XC [auth L] Focus chain Y [auth F] Focus chain YB [auth J] Focus chain Z [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AC [auth J] SDF format, chain CA [auth F] SDF format, chain MC [auth K] SDF format, chain V [auth A] SDF format, chain WC [auth L] SDF format, chain OA [auth G] SDF format, chain OB [auth I] SDF format, chain YA [auth H] MOL2 format, chain AC [auth J] MOL2 format, chain CA [auth F] MOL2 format, chain MC [auth K] MOL2 format, chain V [auth A] MOL2 format, chain WC [auth L] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth I] MOL2 format, chain YA [auth H] mmCIF format, chain AC [auth J] mmCIF format, chain CA [auth F] mmCIF format, chain MC [auth K] mmCIF format, chain V [auth A] mmCIF format, chain WC [auth L] mmCIF format, chain OA [auth G] mmCIF format, chain OB [auth I] mmCIF format, chain YA [auth H]	AC [auth J] CA [auth F] MC [auth K] OA [auth G] OB [auth I] AC [auth J], CA [auth F], MC [auth K], OA [auth G], OB [auth I], V [auth A], WC [auth L], YA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AC [auth J] Focus chain CA [auth F] Focus chain MC [auth K] Focus chain OA [auth G] Focus chain OB [auth I] Focus chain V [auth A] Focus chain WC [auth L] Focus chain YA [auth H] Interactions & Density Focus chain AC [auth J] Focus chain CA [auth F] Focus chain MC [auth K] Focus chain OA [auth G] Focus chain OB [auth I] Focus chain V [auth A] Focus chain WC [auth L] Focus chain YA [auth H]