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Yorodumi- PDB-2yg7: Structure-based redesign of cofactor binding in Putrescine Oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yg7 | ||||||
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Title | Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C-A396T-Q431G Triple 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: 2.75 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 | 2yg7.cif.gz | 357.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yg7.ent.gz | 291.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg7 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg7 | HTTPS FTP |
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-Related structure data
Related structure data | 2yg3SC 2yg4C 2yg5C 2yg6C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: FAD / End label comp-ID: FAD / Refine code: 1 / Auth seq-ID: 2 - 600 / Label seq-ID: 2
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-Components
#1: Protein | Mass: 49387.980 Da / Num. of mol.: 2 / 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): TOP10 / References: UniProt: B0F9F6, putrescine oxidase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 394 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 396 TO THR ...ENGINEERED | |
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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: 2.98 Å3/Da / Density % sol: 45 % / 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: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 31023 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YG3 Resolution: 2.75→98.52 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.84 / SU B: 33.62 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 1.59 / ESU R Free: 0.379 / 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: 33.702 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→98.52 Å
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Refine LS restraints |
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