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Yorodumi- PDB-5c86: Novel fungal alcohol oxidase with catalytic diversity among the A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c86 | ||||||
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Title | Novel fungal alcohol oxidase with catalytic diversity among the AA5 family, apo form | ||||||
Components | Kelch domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / Kelch motif / AA5 / Fungal alcohol oxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Colletotrichum graminicola M1.001 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Urresti, S. / Yin, D.T. / LaFond, M. / Derikvand, F. / Berrin, G.J. / Henrissat, B. / Walton, P.H. / Brumer, H. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Structure-function characterization reveals new catalytic diversity in the galactose oxidase and glyoxal oxidase family. Authors: Yin, D.T. / Urresti, S. / Lafond, M. / Johnston, E.M. / Derikvand, F. / Ciano, L. / Berrin, J.G. / Henrissat, B. / Walton, P.H. / Davies, G.J. / Brumer, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c86.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c86.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 5c86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c86_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 5c86_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 5c86_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 5c86_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c86 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c86 | HTTPS FTP |
-Related structure data
Related structure data | 5c92C 2eieS 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
#1: Protein | Mass: 52386.680 Da / Num. of mol.: 1 / Fragment: UNP residues 25-506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colletotrichum graminicola M1.001 (fungus) Gene: GLRG_05590 / Plasmid: pPICZa-C / Production host: Komagataella pastoris (fungus) / References: UniProt: E3QHV8 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M imidazole, pH 8.0, 12% v/v polyethylene glycol 8.000 and 4.5% 1-butanol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→52.64 Å / Num. all: 72213 / Num. obs: 72213 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.079 / Rsym value: 0.027 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.51→1.55 Å / Redundancy: 10 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2eie Resolution: 1.51→40.53 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.512 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0671 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.069 / SU Rfree Cruickshank DPI: 0.0701 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.419 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→40.53 Å
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Refine LS restraints |
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