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Yorodumi- PDB-6iqz: High resolution structure of bilirubin oxidase from Myrothecium v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iqz | ||||||||||||
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Title | High resolution structure of bilirubin oxidase from Myrothecium verrucaria - wild type | ||||||||||||
Components | Bilirubin oxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / Multicopper oxydase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Myrothecium verrucaria (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||||||||
Authors | Shibata, N. / Akter, M. / Higuchi, Y. | ||||||||||||
Citation | Journal: Chemistry / Year: 2018 Title: Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase. Authors: Akter, M. / Tokiwa, T. / Shoji, M. / Nishikawa, K. / Shigeta, Y. / Sakurai, T. / Higuchi, Y. / Kataoka, K. / Shibata, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iqz.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iqz.ent.gz | 206.4 KB | Display | PDB format |
PDBx/mmJSON format | 6iqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iqz_validation.pdf.gz | 815.8 KB | Display | wwPDB validaton report |
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Full document | 6iqz_full_validation.pdf.gz | 816.7 KB | Display | |
Data in XML | 6iqz_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 6iqz_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqz ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqz | HTTPS FTP |
-Related structure data
Related structure data | 6iqxC 6iqyC 2xllS 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: 60548.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myrothecium verrucaria (fungus) / Plasmid: pPICBO / Production host: Komagataella pastoris (fungus) / References: UniProt: Q12737, bilirubin oxidase |
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-Sugars , 2 types, 2 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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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 542 molecules
#3: Chemical | ChemComp-CU / #5: Chemical | #6: 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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M SODIUM CITRATE PH 5.0, 20% (W/V) PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Oct 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 102516 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.41 |
Reflection shell | Resolution: 1.46→1.49 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XLL Resolution: 1.46→35.712 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→35.712 Å
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Refine LS restraints |
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LS refinement shell |
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