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- PDB-2yg3: Structure-based redesign of cofactor binding in Putrescine Oxidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yg3 | ||||||
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Title | Structure-based redesign of cofactor binding in Putrescine Oxidase: wild type enzyme | ||||||
![]() | PUTRESCINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / FLAVIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kopacz, M.M. / Rovida, S. / van Duijn, E. / Fraaije, M.W. / Mattevi, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.5 KB | Display | ![]() |
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PDB format | ![]() | 164.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961.5 KB | Display | ![]() |
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Full document | ![]() | 975.9 KB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yg4C ![]() 2yg5C ![]() 2yg6C ![]() 2yg7C ![]() 2v5zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 49396.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 100MM MES PH 6.4, 2.2M AMMONIUM SULFATE, 100MM SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2→30 Å / Num. obs: 96941 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V5Z Resolution: 2→98.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.772 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.121 / 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: 16.908 Å2
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Refinement step | Cycle: LAST / Resolution: 2→98.78 Å
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Refine LS restraints |
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