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Yorodumi- PDB-2yku: Structural Determinants of the Beta-Selectivity of a Bacterial Am... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yku | ||||||
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Title | Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase | ||||||
Components | BETA-TRANSAMINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MESORHIZOBIUM SP. LUK (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase. Authors: Wybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yku.cif.gz | 280.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yku.ent.gz | 225.7 KB | Display | PDB format |
PDBx/mmJSON format | 2yku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yku_validation.pdf.gz | 488.8 KB | Display | wwPDB validaton report |
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Full document | 2yku_full_validation.pdf.gz | 496.6 KB | Display | |
Data in XML | 2yku_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 2yku_validation.cif.gz | 87.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/2yku ftp://data.pdbj.org/pub/pdb/validation_reports/yk/2yku | HTTPS FTP |
-Related structure data
Related structure data | 2ykvC 2ykxC 2ykyC 4ao4C 1ohvS 2cy8S 2e7uS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49592.793 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN K280 ETA-AMINE AND THE C4A OF THE PLP COFACTOR Source: (gene. exp.) MESORHIZOBIUM SP. LUK (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A3EYF7 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.36 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.5, 8% V/V ETHYLENE GLYCOL, 10 % W/V PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.35 Å / Num. obs: 129742 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2E7U,2CY8,1OHV Resolution: 1.9→96.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.44 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.688 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→96.03 Å
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Refine LS restraints |
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