+Open data
-Basic information
Entry | Database: PDB / ID: 2o4u | ||||||
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Title | Crystal structure of Mammalian Dimeric Dihydrodiol Dehydrogenase | ||||||
Components | Dimeric dihydrodiol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NADP-binding Rossmann-fold domain / Predominantly anti-parallel Beta sheet | ||||||
Function / homology | Function and homology information D-xylose 1-dehydrogenase (NADP+, D-xylono-1,5-lactone-forming) / D-xylose 1-dehydrogenase (NADP+) activity / D-xylose catabolic process / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Macaca fascicularis (crab-eating macaque) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Carbone, V. / El-Kabbani, O. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structures of dimeric dihydrodiol dehydrogenase apoenzyme and inhibitor complex: probing the subunit interface with site-directed mutagenesis. Authors: Carbone, V. / Endo, S. / Sumii, R. / Chung, R.P. / Matsunaga, T. / Hara, A. / El-Kabbani, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o4u.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o4u.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 2o4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o4u_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 2o4u_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2o4u_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2o4u_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/2o4u ftp://data.pdbj.org/pub/pdb/validation_reports/o4/2o4u | HTTPS FTP |
-Related structure data
Related structure data | 2o48SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36481.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Plasmid: pKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9TQS6, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-BME / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.5M ammonium phosphate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2001 / Details: Bent conical Si-mirror (Rh coated) |
Radiation | Monochromator: Bent conical Si-mirror (Rh coated) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.9 Å / Num. all: 70365 / Num. obs: 37154 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 11.77 / Num. unique all: 6990 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O48 Resolution: 2→19.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.325 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.174 Å2
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Refine analyze | Luzzati coordinate error obs: 0.179 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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