1WUH

Three-Dimensional Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural basis for the activation process of [NiFe] hydrogenase from D.vulgaris Miyazaki F

Ogata, H.Hirota, S.Nakahara, A.Komori, H.Shibata, N.Kato, T.Kano, K.Higuchi, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase small subunit
S
267Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21853
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase large subunit
L
534Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21852
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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

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

Download SDF File 
Download CCD File 
S
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
NFC
Query on NFC

Download SDF File 
Download CCD File 
L
NI-FE ACTIVE CENTER A-FORM
C3 H2 Fe N Ni O4
CIUCFLVMTAQNSJ-HFOLDOAIAB
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
L
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.110 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.227α = 90.00
b = 126.261β = 90.00
c = 66.440γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SHELXL-97refinement
SHELXmodel building
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2019-09-04
    Type: Atomic model, Data collection, Derived calculations