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Yorodumi- PDB-2yg5: Structure-based redesign of cofactor binding in Putrescine Oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yg5 | ||||||
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Title | Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C mutant | ||||||
Components | PUTRESCINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | RHODOCOCCUS ERYTHROPOLIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kopacz, M.M. / Rovida, S. / van Duijn, E. / Fraaije, M.W. / Mattevi, A. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structure-Based Redesign of Cofactor Binding in Putrescine Oxidase. Authors: Kopacz, M.M. / Rovida, S. / Van Duijn, E. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yg5.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yg5.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg5 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg5 | HTTPS FTP |
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-Related structure data
Related structure data | 2yg3SC 2yg4C 2yg6C 2yg7C C: citing same article (ref.) S: Starting model for refinement |
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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: 49429.035 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TOP10 / References: UniProt: B0F9F6, putrescine oxidase | ||||||
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#2: Chemical | ChemComp-FAD / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.11 % / Description: NONE |
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Crystal grow | pH: 6.4 / Details: pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 54711 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YG3 Resolution: 1.9→102.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.939 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.129 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.571 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→102.06 Å
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