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Yorodumi- PDB-3owo: Structures of iron-dependent alcohol dehydrogenase 2 from Zymomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3owo | ||||||
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Title | Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD cofactor | ||||||
Components | Alcohol dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / Alcohol Dehydrogenase 2 / Iron | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / metal ion binding Similarity search - Function | ||||||
Biological species | Zymomonas mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Moon, J.H. / Lee, H.J. / Song, J.M. / Park, S.Y. / Park, M.Y. / Park, H.M. / Sun, J. / Park, J.H. / Kim, J.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD+ cofactor Authors: Moon, J.H. / Lee, H.J. / Park, S.Y. / Song, J.M. / Park, M.Y. / Park, H.M. / Sun, J. / Park, J.H. / Kim, B.Y. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3owo.cif.gz | 297.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3owo.ent.gz | 241 KB | Display | PDB format |
PDBx/mmJSON format | 3owo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3owo_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 3owo_full_validation.pdf.gz | 499.9 KB | Display | |
Data in XML | 3owo_validation.xml.gz | 64.3 KB | Display | |
Data in CIF | 3owo_validation.cif.gz | 90.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/3owo ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3owo | HTTPS FTP |
-Related structure data
Related structure data | 3ox4C 3bfjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40186.098 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ZM4 / Gene: adhB, ZMO1596 / Production host: Escherichia coli (E. coli) References: UniProt: P06758, UniProt: P0DJA2*PLUS, alcohol dehydrogenase #2: Chemical | ChemComp-FE2 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 4000, 0.15M magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2010 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 77861 / % possible obs: 97.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.084 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5 / Num. unique all: 7552 / Rsym value: 0.249 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3BFJ Resolution: 2.07→50 Å / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.07→50 Å
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Refine LS restraints |
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