[English] 日本語
Yorodumi- PDB-2yg6: Structure-based redesign of cofactor binding in Putrescine Oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yg6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure-based redesign of cofactor binding in Putrescine Oxidase: P15I-A394C double 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: 2.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yg6.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yg6.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 2yg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg6 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2yg3SC 2yg4C 2yg5C 2yg7C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
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: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 2 - 450 / Label seq-ID: 2 - 450
|
-Components
#1: Protein | Mass: 49445.078 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: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PRO 15 TO ILE ENGINEERED RESIDUE IN CHAIN A, ALA 394 TO CYS ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 45 % / Description: NONE |
---|---|
Crystal grow | pH: 6.4 / Details: pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.5→30 Å / Num. obs: 51121 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YG3 Resolution: 2.5→51.05 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.996 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.821 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→51.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|