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Yorodumi- PDB-2poq: Dimeric Dihydrodiol Dehydrogenase complexed with inhibitor, Isoas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2poq | |||||||||
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Title | Dimeric Dihydrodiol Dehydrogenase complexed with inhibitor, Isoascorbic acid | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Carbone, V. / El-Kabbani, O. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of monkey dimeric dihydrodiol dehydrogenase in complex with isoascorbic acid. Authors: Carbone, V. / Sumii, R. / Ishikura, S. / Asada, Y. / 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 | 2poq.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2poq.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 2poq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2poq_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 2poq_full_validation.pdf.gz | 473.1 KB | Display | |
Data in XML | 2poq_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2poq_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/2poq ftp://data.pdbj.org/pub/pdb/validation_reports/po/2poq | HTTPS FTP |
-Related structure data
Related structure data | 2o4uS 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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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) Gene: CMO2DD / 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-SO4 / #3: Chemical | ChemComp-BME / | #4: Sugar | ChemComp-ISD / | #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: 3.62 Å3/Da / Density % sol: 66.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2M ammonium sulphate, 0.1 sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→20 Å / Num. all: 17256 / Num. obs: 17128 / % possible obs: 99.26 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.59→2.68 Å / Redundancy: 3.6284 % / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2O4U Resolution: 2.59→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.568 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.324 / ESU R Free: 0.256 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.089 Å2
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Refine analyze | Luzzati coordinate error obs: 0.267 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.659 Å / Total num. of bins used: 20
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