Download MendeleyStructure 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
2FRV
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
- DOI: 10.2210/pdb2FRV/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Desulfovibrio gigas
- Mutation(s): No
- Deposited: 1997-06-10 Released: 1998-06-17
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
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PERIPLASMIC HYDROGENASE | C [auth A], E [auth C], G [auth E], I [auth G], K [auth I], A [auth S] | 264 | Desulfovibrio gigas | Mutation(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 ViewExpand | |||||
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Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PERIPLASMIC HYDROGENASE | D [auth B], F [auth D], H [auth F], J [auth H], L [auth J], B [auth L] | 536 | Desulfovibrio gigas | Mutation(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 ViewExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 Query on SF4 | AA [auth C]
, CA [auth C]
, HA [auth E]
, JA [auth E]
, M [auth S]
, O [auth S]
, OA [auth G]
, QA [auth G]
, | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC |  | Ligand Interaction | |
| F3S Query on F3S | 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 | 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 | 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 | 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 | 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 = 112.78 | α = 90.03 |
| b = 113.16 | β = 90.02 |
| c = 133.91 | γ = 119.99 |
| Software Name | Purpose |
|---|---|
| MOSFLM | data reduction |
| CCP4 | data reduction |
| AMoRE | phasing |
| PROLSQ | refinement |
| CCP4 | data scaling |
Entry History
Deposition Data
- Deposited Date: 1997-06-10
- Released Date: 1998-06-17 Deposition Author(s): Volbeda, A., Frey, M., Fontecilla-Camps, J.C.
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
