6ZLF

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 
  • R-Value Work: 0.182 

Starting Model: experimental
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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)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]
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
FEO
Query on FEO

Download Ideal Coordinates CCD File 
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
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
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
KR
Query on KR

Download Ideal Coordinates CCD File 
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
CL
Query on CL

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.182 
  • 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 


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