6ZK8

Native crystal structure of anaerobic F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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

  • 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)A,
B [auth O]
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 
AA [auth O],
J [auth A]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
1PE
Query on 1PE

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F [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG
Query on PEG

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C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth A]
C [auth A],
D [auth A],
E [auth A],
G [auth A],
H [auth A],
Q [auth O],
R [auth O]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth O],
T [auth O],
U [auth O],
V [auth O],
W [auth O],
X [auth O]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
I [auth A],
P [auth A],
Y [auth O],
Z [auth O]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.871α = 90
b = 156.609β = 137.62
c = 76.065γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceLn23 ANR- 13-BS07-0007-01
Max Planck SocietyGermanyMax Planck Gessellschaft

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