+
Open data
-
Basic information
Entry | Database: PDB / ID: 2frv | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE | ||||||
![]() | (PERIPLASMIC HYDROGENASE) x 2 | ||||||
![]() | OXIDOREDUCTASE / NI-FE HYDROGENASE | ||||||
Function / homology | ![]() cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C. | ||||||
![]() | Journal: J.Am.Chem.Soc. / Year: 1996 Title: Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands Authors: Volbeda, A. / Garcin, E. / Piras, C. / De Lacey, A.L. / Fernandez, V.M. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C. #1: ![]() Title: Gas Access to the Active Site of Ni-Fe Hydrogenases Probed by X-Ray Crystallography and Molecular Dynamics Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C. #2: ![]() Title: Crystal Structure of the Nickel-Iron Hydrogenase from Desulfovibrio Gigas Authors: Volbeda, A. / Charon, M.H. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 904.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 741.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 678.8 KB | Display | |
Data in XML | ![]() | 109.6 KB | Display | |
Data in CIF | ![]() | 166.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1frvS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||
3 | ![]()
| ||||||||||||||||||||||||
4 | ![]()
| ||||||||||||||||||||||||
5 | ![]()
| ||||||||||||||||||||||||
6 | ![]()
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||||||||||
Details | THERE ARE SIX MOLECULES PER (TRICLINIC) UNIT CELL. EACH OF THESE CONSISTS OF ONE SMALL AND ONE LARGE SUBUNIT. IN ALL STAGES THE SIX HYDROGENASE MOLECULES WERE CONSTRAINED TO OBEY EXACT NON-CRYSTALLOGRAPHIC SYMMETRY. |
-
Components
-Protein , 2 types, 12 molecules SACEGILBDFHJ
#1: Protein | Mass: 28351.396 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 59571.938 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 7 types, 1188 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-F3S / #5: Chemical | ChemComp-NI / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-FCO / #8: Chemical | ChemComp-O / #9: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | THE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY ...THE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE LATTER ASSIGNMENT |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % |
---|---|
Crystal grow | pH: 6.6 / Details: pH 6.6 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.905 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→29.36 Å / Num. obs: 174383 / % possible obs: 92.5 % / Observed criterion σ(I): 4 / Redundancy: 1.7 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.54→2.84 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4 / % possible all: 87.4 |
Reflection | *PLUS Num. measured all: 296283 |
Reflection shell | *PLUS % possible obs: 87.4 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FRV, MOLECULE 1 Resolution: 2.54→8 Å / Cross valid method: R-FREE / σ(F): 0 / Details: BEFORE PROLSQ: AMORE + X-PLOR
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|