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Download EndnoteStructure 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
- 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
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| PERIPLASMIC HYDROGENASE | S, A, C, E, G, I | 264 | Desulfovibrio gigas | Mutation(s): 0 Gene Names: hydA EC: 1.12.2.1 |
Find proteins for P12943 (Desulfovibrio gigas) Go to UniProtKB: P12943 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| PERIPLASMIC HYDROGENASE | L, B, D, F, H, J | 536 | Desulfovibrio gigas | Mutation(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 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 Query on SF4 | A, C, E, G, I, S | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC |  | Ligand Interaction | |
| F3S Query on F3S | A, C, E, G, I, S | FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW |  | Ligand Interaction | |
| FCO Query on FCO | B, D, F, H, J, L | CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N |  | Ligand Interaction | |
| O Query on O | B, D, F, H, J, L | OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N |  | Ligand Interaction | |
| MG Query on MG | B, D, F, H, J, L | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| NI Query on NI | 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 = 112.780 | α = 90.03 |
| b = 113.160 | β = 90.02 |
| c = 133.910 | γ = 119.99 |
| Software Name | Purpose |
|---|---|
| CCP4 | data reduction |
| AMoRE | phasing |
| PROLSQ | refinement |
| CCP4 | data scaling |
| MOSFLM | data reduction |
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
- 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
