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Yorodumi- PDB-2efu: The crystal structure of D-amino acid amidase from Ochrobactrum a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2efu | ||||||
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Title | The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine | ||||||
Components | D-Amino acid amidase | ||||||
Keywords | HYDROLASE / penicillin recognizing proteins / D-stereospecific / amidase / L-phenylalanine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ochrobactrum anthropi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Okazaki, S. / Suzuki, A. / Mizushima, T. / Komeda, H. / Asano, Y. / Yamane, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3. Authors: Okazaki, S. / Suzuki, A. / Mizushima, T. / Komeda, H. / Asano, Y. / Yamane, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efu.cif.gz | 443.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efu.ent.gz | 359.7 KB | Display | PDB format |
PDBx/mmJSON format | 2efu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2efu_validation.pdf.gz | 493.8 KB | Display | wwPDB validaton report |
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Full document | 2efu_full_validation.pdf.gz | 516.6 KB | Display | |
Data in XML | 2efu_validation.xml.gz | 88.7 KB | Display | |
Data in CIF | 2efu_validation.cif.gz | 125.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efu ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efu | HTTPS FTP |
-Related structure data
Related structure data | 2efxC 2drwS 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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Unit cell |
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-Components
#1: Protein | Mass: 40127.191 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: SV3 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9LCC8 #2: Chemical | ChemComp-BA / #3: Chemical | ChemComp-PHE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 93589 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Rsym value: 0.096 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DAA native structure (2DRW) Resolution: 2.3→47.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.647 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.247 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.417 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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