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Yorodumi- PDB-2ykv: Structural Determinants of the Beta-Selectivity of a Bacterial Am... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ykv | ||||||
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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 | 2ykv.cif.gz | 267.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ykv.ent.gz | 214.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ykv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/2ykv ftp://data.pdbj.org/pub/pdb/validation_reports/yk/2ykv | HTTPS FTP |
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-Related 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 oper:
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-Components
#1: Protein | Mass: 49592.793 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MESORHIZOBIUM SP. LUK (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A3EYF7 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Nonpolymer details | IK2: LINK BETWEEN THE C4A ATOM OF THE PLP COFACTOR AND THE AMINE-GROUP OF 2-AMINOOXYAC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.77 % / Description: USING RIGID BODY REFINEMENT |
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Crystal grow | Details: SAME AS WILD-TYPE APO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.09 Å / Num. obs: 125289 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MES_BFAT_APO Resolution: 1.9→48.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.709 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / 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: 21.784 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.09 Å
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Refine LS restraints |
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