4TTT

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase

Kalms, J.Schmidt, A.Frielingsdorf, S.Utesch, T.Gotthard, G.von Stetten, D.van der Linden, P.Royant, A.Mroginski, M.Carpentier, P.Lenz, O.Scheerer, P.

(2018) Proc Natl Acad Sci U S A 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uptake hydrogenase large subunit hoxGL603Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxGPHG002
EC: 1.12.99.6
Find proteins for P31891 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Explore P31891 
Go to UniProtKB:  P31891
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uptake hydrogenase small subunit hoxKS339Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxKPHG001
EC: 1.12.99.6
Find proteins for P31892 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Explore P31892 
Go to UniProtKB:  P31892
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download CCD File 
S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F4S
Query on F4S

Download CCD File 
S
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFV
Query on NFV

Download CCD File 
L
NI-FE OXIDIZED ACTIVE CENTER
C3 Fe N2 Ni O2
MPQMGFDSXFFIQL-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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L, S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.774α = 90
b = 95.57β = 90
c = 119.228γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UNICATGermany--

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary