6LL4 | pdb_00006ll4

Oxygen-exposed carbazole-soaked reduced terminal oxygenase of carbazole 1,9a-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb6LL4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Janthinobacterium sp. J3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-21 Released: 2021-01-27
Deposition Author(s): Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.244 (DCC)
R-Value Work:
0.169 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

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

Oxygen-exposed carbazole-soaked reduced terminal oxygenase of carbazole 1,9a-dioxygenase with

Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.

To be published.

Macromolecule Content

Total Structure Weight: 139.45 kDa
Atom Count: 10,038
Modeled Residue Count: 1,149
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal oxygenase component of carbazole	A, B, C	392	Janthinobacterium sp. J3	Mutation(s): 0 Gene Names: carAa
UniProt
Find proteins for Q84II6 (Janthinobacterium sp. (strain J3)) Explore Q84II6 Go to UniProtKB: Q84II6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84II6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9G0 Query on 9G0 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain SA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain SA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain SA [auth C]	SA [auth C], V [auth B]	2'-amino[1,1'-biphenyl]-2,3-diol C₁₂ H₁₁ N O₂ WPDDFIBFWKUENN-UHFFFAOYSA-N		Interactions Focus chain SA [auth C] Focus chain V [auth B] Interactions & Density Focus chain SA [auth C] Focus chain V [auth B]
EHX Query on EHX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(9aR)-9a-(dioxidanyl)-1,9-dihydrocarbazole C₁₂ H₁₁ N O₂ UZUUDVVIIUNBSP-GFCCVEGCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain QA [auth C] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain T [auth B] mmCIF format, chain D [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain T [auth B]	D [auth A], QA [auth C], T [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain QA [auth C] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain QA [auth C] Focus chain T [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain ZA [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain ZA [auth C]	NA [auth B], P [auth A], Q [auth A], R [auth A], ZA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain NA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain ZA [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain YA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain YA [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain YA [auth C]	HA [auth B] IA [auth B] JA [auth B] KA [auth B] L [auth A] HA [auth B], IA [auth B], JA [auth B], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], YA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain YA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain YA [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain S [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain S [auth A]	OA [auth B], PA [auth B], S [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain OA [auth B] Focus chain PA [auth B] Focus chain S [auth A] Interactions & Density Focus chain OA [auth B] Focus chain PA [auth B] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], X [auth B], XA [auth C], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain RA [auth C] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain U [auth B] mmCIF format, chain E [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain U [auth B]	E [auth A], RA [auth C], U [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain RA [auth C] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain RA [auth C] Focus chain U [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]