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Yorodumi- PDB-1gqh: Quercetin 2,3-dioxygenase in complex with the inhibitor kojic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gqh | |||||||||
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Title | Quercetin 2,3-dioxygenase in complex with the inhibitor kojic acid | |||||||||
Components | QUERCETIN 2,3-DIOXYGENASE | |||||||||
Keywords | OXIDOREDUCTASE / DIOXYGENASE | |||||||||
Function / homology | Function and homology information quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ASPERGILLUS JAPONICUS (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å | |||||||||
Authors | Steiner, R.A. / Dijkstra, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase.1.Ligand-Induced Coordination Changes Probed by X-Ray Crystallography: Inhibition, Ordering Effect and Mechanistic Insights Authors: Steiner, R.A. / Kooter, I.M. / Dijkstra, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gqh.cif.gz | 287.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqh.ent.gz | 238.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqh_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1gqh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1gqh_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 1gqh_validation.cif.gz | 87.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqh ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqh | HTTPS FTP |
-Related 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37958.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS JAPONICUS (mold) / Production host: ASPERGILLUS AWAMORI (mold) / References: UniProt: Q7SIC2*PLUS, quercetin 2,3-dioxygenase |
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-Sugars , 4 types, 16 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 1027 molecules
#5: Chemical | ChemComp-KOJ / #6: Chemical | ChemComp-CU / #8: 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: 2.32 Å3/Da / Density % sol: 46.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.2 Details: HANGING DROP, 21-23% PEG 8000, 200 MM AMMONIUM SULFATE, 100 MM CITRATE BUFFER, PH 5.2, 10 MM NA DIETHYLDITHIOCARBAMATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→38.07 Å / Num. obs: 72101 / % possible obs: 89.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3 / % possible all: 86.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 150878 / Rmerge(I) obs: 0.13 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.15→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.751 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49.39 Å
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