+Open data
-Basic information
Entry | Database: PDB / ID: 4mom | ||||||
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Title | Pyranose 2-oxidase H450G mutant with 3-fluorinated galactose | ||||||
Components | Pyranose 2-oxidase | ||||||
Keywords | OXIDOREDUCTASE / GMC OXIDOREDUCTASE / PHBH FOLD / HOMOTETRAMER / FAD-BINDING / SUBSTRATE COMPLEX / FLAVINYLATION / INTRACELLULAR | ||||||
Function / homology | Function and homology information pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space Similarity search - Function | ||||||
Biological species | Trametes ochracea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion. Authors: Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mom.cif.gz | 897.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mom.ent.gz | 754.4 KB | Display | PDB format |
PDBx/mmJSON format | 4mom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mom_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4mom_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4mom_validation.xml.gz | 95.7 KB | Display | |
Data in CIF | 4mom_validation.cif.gz | 133.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/4mom ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mom | HTTPS FTP |
-Related structure data
Related structure data | 4moeC 4mofC 4mogC 4mohC 4moiC 4mojC 4mokC 4molC 4mooC 4mopC 4moqC 4morC 4mosC 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
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 70472.961 Da / Num. of mol.: 4 / Mutation: H450G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes ochracea (fungus) / Gene: p2o / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase #3: Sugar | ChemComp-2H5 / |
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-Non-polymers , 4 types, 1077 molecules
#2: Chemical | ChemComp-FDA / #4: Chemical | ChemComp-1PE / #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: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M MES, 50 mM MgCl2, 10% (w/v) monomethylether PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2009 / Details: Rh-coated Si mirrors |
Radiation | Monochromator: Double-crystal monochromator, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.14 Å / Num. all: 215840 / Num. obs: 215840 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.92 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.163 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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