6ZLF | pdb_00006zlf

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


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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view details

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coenzyme F420H2 oxidase (FprA)410Methanothermococcus thermolithotrophicusMutation(s): 0 
UniProt
Find proteins for A0A452CSW8 (Methanothermococcus thermolithotrophicus)
Explore A0A452CSW8 
Go to UniProtKB:  A0A452CSW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A452CSW8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
BA [auth F]
LC [auth K]
NA [auth G]
NB [auth I]
U [auth A]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
FEO
Query on FEO

Download Ideal Coordinates CCD File 
BB [auth I]
CC [auth K]
EA [auth F]
GA [auth G]
J [auth A]
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AB [auth I]
BC [auth K]
CB [auth I]
DA [auth F]
DB [auth I]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
KR
Query on KR

Download Ideal Coordinates CCD File 
AA [auth F]
FC [auth K]
GB [auth I]
GC [auth K]
HB [auth I]
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AC [auth J]
CA [auth F]
MC [auth K]
OA [auth G]
OB [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.025α = 90
b = 162.553β = 93.75
c = 134.376γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance13-BS07-0007-01
Max Planck SocietyGermanyMax Planck Gesellschaft

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description