2FRV

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands

Volbeda, A.Garcin, E.Piras, C.De Lacey, A.L.Fernandez, V.M.Hatchikian, E.C.Frey, M.Fontecilla-Camps, J.C.

(1996) J.Am.Chem.Soc. 118: 12989


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC HYDROGENASE
S, A, C, E, G, I
264Desulfovibrio gigasMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P12943 (Desulfovibrio gigas)
Go to UniProtKB:  P12943
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC HYDROGENASE
L, B, D, F, H, J
536Desulfovibrio gigasMutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P12944 (Desulfovibrio gigas)
Go to UniProtKB:  P12944
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, C, E, G, I, S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, C, E, G, I, S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download SDF File 
Download CCD File 
B, D, F, H, J, L
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download SDF File 
Download CCD File 
B, D, F, H, J, L
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, D, F, H, J, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B, D, F, H, J, L
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 112.780α = 90.03
b = 113.160β = 90.02
c = 133.910γ = 119.99
Software Package:
Software NamePurpose
CCP4data reduction
AMoREphasing
PROLSQrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance