+Open data
-Basic information
Entry | Database: PDB / ID: 1juh | |||||||||
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Title | Crystal Structure of Quercetin 2,3-dioxygenase | |||||||||
Components | quercetin 2,3-dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / dioxygenase / CUPIN / GLYCOPROTEIN / beta sandwich | |||||||||
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 / MIRAS / Resolution: 1.6 Å | |||||||||
Authors | Fusetti, F. / Schroeter, K.H. / Steiner, R.A. / Dijkstra, B.W. | |||||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Authors: Fusetti, F. / Schroter, K.H. / Steiner, R.A. / van Noort, P.I. / Pijning, T. / Rozeboom, H.J. / Kalk, K.H. / Egmond, M.R. / 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 | 1juh.cif.gz | 316.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1juh.ent.gz | 258.6 KB | Display | PDB format |
PDBx/mmJSON format | 1juh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1juh_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1juh_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1juh_validation.xml.gz | 67 KB | Display | |
Data in CIF | 1juh_validation.cif.gz | 102.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1juh ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1juh | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 natural source / Source: (natural) Aspergillus japonicus (mold) / References: UniProt: Q7SIC2, quercetin 2,3-dioxygenase |
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-Sugars , 5 types, 17 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-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 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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 |
#4: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-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 |
#5: 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 / |
-Non-polymers , 3 types, 1790 molecules
#7: Chemical | ChemComp-CU / #8: Chemical | ChemComp-EDO / #9: 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 | pH: 5.2 Details: HANGING DROP, 22-26% PEG 8000, 200 MM AMMONIUM SULFATE, 100 MM CITRATE BUFFER, PH 5.2 | ||||||||||||||||||||||||||||||||||||
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: 0.84 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 1998 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→87.7 Å / Num. obs: 234572 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 9.45 % / Biso Wilson estimate: 17.26 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.5 / % possible all: 84.7 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / % possible obs: 95 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.6→87.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 20.88 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→87.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.26 / Rfactor obs: 0.26 |