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 
  • R-Value Observed: 0.202 

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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC HYDROGENASEC [auth A], E [auth C], G [auth E], I [auth G], K [auth I], A [auth S]264Desulfovibrio gigasMutation(s): 0 
Gene Names: hydA
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12943 (Desulfovibrio gigas)
Explore P12943 
Go to UniProtKB:  P12943
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC HYDROGENASED [auth B], F [auth D], H [auth F], J [auth H], L [auth J], B [auth L]536Desulfovibrio gigasMutation(s): 0 
Gene Names: hydB
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12944 (Desulfovibrio gigas)
Explore P12944 
Go to UniProtKB:  P12944
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth C] , CA [auth C] , HA [auth E] , JA [auth E] , M [auth S] , O [auth S] , OA [auth G] , QA [auth G] , 
AA [auth C],  CA [auth C],  HA [auth E],  JA [auth E],  M [auth S],  O [auth S],  OA [auth G],  QA [auth G],  T [auth A],  V [auth A],  VA [auth I],  XA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
BA [auth C], IA [auth E], N [auth S], PA [auth G], U [auth A], WA [auth I]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
AB [auth J], FA [auth D], MA [auth F], R [auth L], TA [auth H], Y [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
DA [auth D], KA [auth F], P [auth L], RA [auth H], W [auth B], YA [auth J]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth D], LA [auth F], Q [auth L], SA [auth H], X [auth B], ZA [auth J]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download Ideal Coordinates CCD File 
BB [auth J], GA [auth D], NA [auth F], S [auth L], UA [auth H], Z [auth B]OXYGEN ATOM
O
XLYOFNOQVPJJNP-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 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.78α = 90.03
b = 113.16β = 90.02
c = 133.91γ = 119.99
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
PROLSQrefinement
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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