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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC HYDROGENASE264Desulfovibrio gigasMutation(s): 0 
Gene Names: hydA
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12943 (Megalodesulfovibrio gigas)
Explore P12943 
Go to UniProtKB:  P12943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12943
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC HYDROGENASE536Desulfovibrio gigasMutation(s): 0 
Gene Names: hydB
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12944 (Megalodesulfovibrio gigas)
Explore P12944 
Go to UniProtKB:  P12944
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12944
Protein Feature View
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  • 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],
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

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BA [auth C],
IA [auth E],
N [auth S],
PA [auth G],
U [auth A],
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],
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

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DA [auth D],
KA [auth F],
P [auth L],
RA [auth H],
W [auth B],
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

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EA [auth D],
LA [auth F],
Q [auth L],
SA [auth H],
X [auth B],
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],
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