+Open data
-Basic information
Entry | Database: PDB / ID: 8jpz | |||||||||
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Title | The thermostability mutant Gox_M8 from Aspergillus niger | |||||||||
Components | Glucose oxidase (Fragment) | |||||||||
Keywords | OXIDOREDUCTASE / Glucose oxidase | |||||||||
Function / homology | Function and homology information glucose oxidase / glucose oxidase activity / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | Aspergillus niger (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||
Authors | Tu, T. / Yan, Y.R. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Revealing the pH-Dependent Activity Mechanism of a Ferrari Oxidoreductase Enzyme-Glucose Oxidase Authors: Tu, T. / Yan, Y.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jpz.cif.gz | 329.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jpz.ent.gz | 212.3 KB | Display | PDB format |
PDBx/mmJSON format | 8jpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/8jpz ftp://data.pdbj.org/pub/pdb/validation_reports/jp/8jpz | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63154.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q5Q041 |
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-Sugars , 2 types, 13 molecules
#2: Polysaccharide | #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 869 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | ChemComp-MPD / ( | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M sodium chloride, 0.1 M HEPES buffer (pH 7.0), and 12% (w/v) polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→21.18 Å / Num. obs: 94279 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 36.31 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.86 |
Reflection shell | Resolution: 2.08→2.154 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 9278 / CC1/2: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→21.18 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6575 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→21.18 Å
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Refine LS restraints |
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LS refinement shell |
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