[English] 日本語
Yorodumi- PDB-1ubk: Three-dimensional Structure of The Carbon Monoxide Complex of [Ni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ubk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F | |||||||||
Components | (Periplasmic [NiFe] hydrogenase ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / High resolution crystal structure / [NiFe]hydrogenase / Carbon Monoxide Complex | |||||||||
Function / homology | Function and homology information 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 | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.18 Å | |||||||||
Authors | Ogata, H. / Mizoguchi, Y. / Mizuno, N. / Miki, K. / Adachi, S. / Yasuoka, N. / Yagi, T. / Yamauchi, O. / Hirota, S. / Higuchi, Y. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen Authors: Ogata, H. / Mizoguchi, Y. / Mizuno, N. / Miki, K. / Adachi, S. / Yasuoka, N. / Yagi, T. / Yamauchi, O. / Hirota, S. / Higuchi, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ubk.cif.gz | 371.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ubk.ent.gz | 300 KB | Display | PDB format |
PDBx/mmJSON format | 1ubk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ubk_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ubk_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 1ubk_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1ubk_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/1ubk ftp://data.pdbj.org/pub/pdb/validation_reports/ub/1ubk | HTTPS FTP |
-Related structure data
Related structure data | 1ubhC 1ubjC 1ublC 1ubmC 1uboC 1ubrC 1ubtC 1ubuC 1h2rS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules SL
#1: Protein | Mass: 28789.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki F / References: UniProt: P21853, cytochrome-c3 hydrogenase |
---|---|
#2: Protein | Mass: 59208.398 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-552 / Source method: isolated from a natural source Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki F / References: UniProt: P21852, cytochrome-c3 hydrogenase |
-Non-polymers , 7 types, 1072 molecules
#3: Chemical | #4: Chemical | ChemComp-F3S / | #5: Chemical | ChemComp-MPD / ( #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-FNE / ( | #8: Chemical | ChemComp-CMO / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: MPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
Crystal grow | *PLUS |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 17, 2000 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→27.455 Å / Num. all: 252083 / Num. obs: 230808 / % possible obs: 87.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 1.18→1.25 Å / Rmerge(I) obs: 0.339 / % possible all: 68.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1H2R Resolution: 1.18→20 Å / Num. parameters: 66023 / Num. restraintsaints: 79672 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 298 / Occupancy sum non hydrogen: 7290.92 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→20 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.117 / Rfactor Rfree: 0.151 / Rfactor Rwork: 0.117 / Highest resolution: 1.2 Å / Num. reflection obs: 214464 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.25 Å / Rfactor Rwork: 0.194 |