1FRF

CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS

Structural Biology Knowledgebase: 1FRF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1FRF

Classification: OXIDOREDUCTASE

Total Structure Weight: 91230.59

Macromolecule Entities
Molecule Chains Length Organism Details
[NI-FE] HYDROGENASE S 264 Desulfovibrio fructosivorans EC#: 1.12.2.1 IUBMB
Fragment: SMALL CHAIN
Mutation: Q62E, T98C, R113T, H114C, L115S, H117Y
Gene Name(s): hydA
[NI-FE] HYDROGENASE L 564 Desulfovibrio fructosivorans EC#: 1.12.2.1 IUBMB
Fragment: LARGE CHAIN
Mutation: C353G
Gene Name(s): hydB

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

S IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

S FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

L NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

L FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

L MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.220
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 65.61 α = 90.00
b = 99.77 β = 90.88
c = 184.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-07-21
  • Released Date: 1998-07-29
  • Deposition author(s): Montet, Y., Volbeda, A., Piras, C., Hatchikian, E.C., Frey, M., Fontecilla, J.C.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4