[English] 日本語
![](img/lk-miru.gif)
- PDB-5jsu: The 3D structure of the U489C variant of [NiFeSe] hydrogenase fro... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jsu | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The 3D structure of the U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the oxidized state at 1.40 Angstrom resolution | ||||||||||||
![]() | (Periplasmic [NiFeSe] hydrogenase, ...) x 2 | ||||||||||||
![]() | OXIDOREDUCTASE / NIFESE-SITE H2 CLEAVAGE/PRODUCTION | ||||||||||||
Function / homology | ![]() cytochrome-c3 hydrogenase / ferredoxin 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 ...cytochrome-c3 hydrogenase / ferredoxin 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Marques, M.C. / Pereira, I.A.C. / Matias, P.M. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis. Authors: Marques, M.C. / Tapia, C. / Gutierrez-Sanz, O. / Ramos, A.R. / Keller, K.L. / Wall, J.D. / De Lacey, A.L. / Matias, P.M. / Pereira, I.A.C. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 463.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 380.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5jshC ![]() 5jskC ![]() 5jsyC ![]() 5jt1C ![]() 3ze9S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Periplasmic [NiFeSe] hydrogenase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33940.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hysB, DVU_1917 Production host: ![]() References: UniProt: Q72AS4, ferredoxin hydrogenase |
---|---|
#2: Protein | Mass: 55942.148 Da / Num. of mol.: 1 / Mutation: U489C Source method: isolated from a genetically manipulated source Details: Cys489 oxidized to sulfinate (CSD) in crystal structure Source: (gene. exp.) ![]() Gene: hysA, DVU_1918 Production host: ![]() References: UniProt: Q72AS3, ferredoxin hydrogenase |
-Non-polymers , 7 types, 720 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/6ML.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6ML.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-6ML / | #5: Chemical | ChemComp-FCO / | #6: Chemical | #7: Chemical | ChemComp-NI / | #8: Chemical | ChemComp-FE2 / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.38 % / Description: irregular hexagonal plate |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9701 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.4 Å / Num. obs: 136125 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 88.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ZE9 Resolution: 1.4→45.362 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 12.11 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.362 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|