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- PDB-6i3j: Bilirubin oxidase from Myrothecium verrucaria in complex with fer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i3j | ||||||||||||||||||
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Title | Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide | ||||||||||||||||||
![]() | Bilirubin oxidase | ||||||||||||||||||
![]() | OXIDOREDUCTASE / Trp-His cross link / complex | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Svecova, L. / Koval, T. / Skalova, T. / Kolenko, P. / Duskova, J. / Ostergaard, L.H. / Dohnalek, J. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.3 KB | Display | ![]() |
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PDB format | ![]() | 197.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 66.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i3kC ![]() 6i3lC ![]() 2xllS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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 ![](data/chem/img/CU.gif)
![](data/chem/img/FC6.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FC6.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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