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Yorodumi- PDB-3eev: Crystal Structure of Chloramphenicol Acetyltransferase VCA0300 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eev | ||||||
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Title | Crystal Structure of Chloramphenicol Acetyltransferase VCA0300 from Vibrio cholerae O1 biovar eltor | ||||||
Components | Chloramphenicol acetyltransferase | ||||||
Keywords | TRANSFERASE / beta-helix / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information chloramphenicol O-acetyltransferase / acyltransferase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Chloramphenicol Acetyltransferase VCA0300 from Vibrio cholerae O1 biovar eltor Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eev.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eev.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/3eev ftp://data.pdbj.org/pub/pdb/validation_reports/ee/3eev | HTTPS FTP |
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-Related structure data
Related structure data | 2xatS 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: 23845.730 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: catB9, VC_A0300 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9KMN1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Ammonium phosphate, 0.1 M TRIS pH 8.5, 50 %v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Aug 11, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→32.7 Å / Num. all: 22994 / Num. obs: 22994 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 48.67 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1129 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xat Resolution: 2.61→32.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 22.715 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.027 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 44.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→32.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.673 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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