+Open data
-Basic information
Entry | Database: PDB / ID: 4beu | |||||||||
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Title | Structure of Vibrio cholerae broad spectrum racemase | |||||||||
Components | ALANINE RACEMASE | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information methionine racemase activity / ornithine racemase activity / arginine racemase activity / lysine racemase activity / amino-acid racemase / serine racemase activity / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding ...methionine racemase activity / ornithine racemase activity / arginine racemase activity / lysine racemase activity / amino-acid racemase / serine racemase activity / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / periplasmic space / cytosol Similarity search - Function | |||||||||
Biological species | VIBRIO CHOLERAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Carrasco-Lopez, C. / Hermoso, J.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases. Authors: Espaillat, A. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Pietrosemoli, N. / Otero, L.H. / Alvarez, L. / De Pedro, M.A. / Pazos, F. / Davis, B.M. / Waldor, M.K. / Hermoso, J.A. / Cava, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4beu.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4beu.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 4beu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4beu_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 4beu_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 4beu_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4beu_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4beu ftp://data.pdbj.org/pub/pdb/validation_reports/be/4beu | HTTPS FTP |
-Related structure data
Related structure data | 4beqC 4bf5C 4bhyC 2rjgS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42641.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D0H7Y0, UniProt: Q9KSE5*PLUS, alanine racemase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM IODIDE, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95994 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95994 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→47.3 Å / Num. obs: 128145 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 10.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.3 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RJG Resolution: 1.15→47.399 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 16.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.642 Å2 / ksol: 0.442 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→47.399 Å
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Refine LS restraints |
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LS refinement shell |
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