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Yorodumi- PDB-1gqg: Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gqg | |||||||||
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Title | Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldithiocarbamate | |||||||||
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: 1.7 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 | 1gqg.cif.gz | 295.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqg.ent.gz | 245.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1gqg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1gqg_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 1gqg_validation.cif.gz | 95.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqg ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqg | 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 , 3 types, 16 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 1452 molecules
#4: Chemical | ChemComp-DCD / #5: Chemical | ChemComp-CU / #7: 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.845 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.92 Å / Num. obs: 148198 / % possible obs: 91.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.5 / % possible all: 69.4 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 91.1 % / Num. measured all: 637059 |
Reflection shell | *PLUS % possible obs: 69.4 % |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.7→19.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.009 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / 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: 1.7→19.92 Å
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Refine LS restraints |
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