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Yorodumi- PDB-3qvp: Crystal structure of glucose oxidase for space group C2221 at 1.2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qvp | |||||||||
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Title | Crystal structure of glucose oxidase for space group C2221 at 1.2 A resolution | |||||||||
Components | Glucose oxidase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information glucose oxidase / glucose oxidase activity / flavin adenine dinucleotide binding / extracellular region Similarity search - Function | |||||||||
Biological species | Aspergillus niger (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Kommoju, P. / Chen, Z. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Authors: Kommoju, P.R. / Chen, Z.W. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: 1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes. Authors: Wohlfahrt, G. / Witt, S. / Hendle, J. / Schomburg, D. / Kalisz, H.M. / Hecht, H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qvp.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qvp.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qvp ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qvp | HTTPS FTP |
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-Related structure data
Related structure data | 3qseC 3qsmC 3qssC 3qvrC 1cf3S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63329.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Gene: gox / References: UniProt: P13006, glucose oxidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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 |
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#3: Sugar |
-Non-polymers , 5 types, 1300 molecules
#4: Chemical | ChemComp-FAD / |
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#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-PEG / |
#7: Chemical | ChemComp-CL / |
#8: 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: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 200 mM NaCl and 20% PEG 3350, pH 6.9, 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: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: APS Biocars 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→40 Å / Num. all: 184957 / Num. obs: 179408 / % possible obs: 97 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 5.8 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 23.1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CF3 Resolution: 1.2→18.61 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 240549.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.4527 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→18.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.28 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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