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Yorodumi- PDB-6i3j: Bilirubin oxidase from Myrothecium verrucaria in complex with fer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i3j | ||||||||||||||||||
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Title | Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide | ||||||||||||||||||
Components | Bilirubin oxidase | ||||||||||||||||||
Keywords | OXIDOREDUCTASE / Trp-His cross link / complex | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Albifimbria verrucaria (fungus) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||||||||||||||
Authors | Svecova, L. / Koval, T. / Skalova, T. / Kolenko, P. / Duskova, J. / Ostergaard, L.H. / Dohnalek, J. | ||||||||||||||||||
Funding support | Czech Republic, 5items
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Citation | Journal: Sci Rep / Year: 2019 Title: Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer. Authors: Koval, T. / Svecova, L. / Ostergaard, L.H. / Skalova, T. / Duskova, J. / Hasek, J. / Kolenko, P. / Fejfarova, K. / Stransky, J. / Trundova, M. / Dohnalek, J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i3j.cif.gz | 248.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i3j.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 6i3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i3j ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i3j | HTTPS FTP |
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-Related structure data
Related structure data | 6i3kC 6i3lC 2xllS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36i3j / Data set type: diffraction image 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60009.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Albifimbria verrucaria (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: Q12737, bilirubin oxidase |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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-(1-3)-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 |
#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 |
-Non-polymers , 7 types, 579 molecules
#6: Chemical | ChemComp-CU / #7: Chemical | ChemComp-FC6 / #8: Chemical | ChemComp-SIN / #9: Chemical | ChemComp-NA / #10: Chemical | ChemComp-CL / | #11: Chemical | ChemComp-PGR / | #12: 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: 3.25 Å3/Da / Density % sol: 62.1 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.1 Details: 14% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→47.3 Å / Num. obs: 48305 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 6.5 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.061 / Rrim(I) all: 0.157 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.59→2.67 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2 / Num. unique obs: 4411 / CC1/2: 0.608 / Rpim(I) all: 0.428 / Rrim(I) all: 0.963 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XLL Resolution: 2.59→47.3 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 7.185 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.271 Stereochemistry target values: STEREOCHEMISTRY LIBRARY OF CCP4 v. 7.0, LIBRARY FOR FC6 ACCORDING TO CSD RELEASE 5.39 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.142 Å2
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Refinement step | Cycle: 1 / Resolution: 2.59→47.3 Å
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Refine LS restraints |
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