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Yorodumi- PDB-3p2m: Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p2m | ||||||
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Title | Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis | ||||||
Components | POSSIBLE HYDROLASE | ||||||
Keywords | HYDROLASE / Alpha/beta hydrolase superfamily | ||||||
Function / homology | Alpha/beta hydrolase family / carboxylic ester hydrolase activity / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Zheng, X.D. / Guo, J. / Xu, L. / Li, H. / Zhang, D. / Zhang, K. / Sun, F. / Wen, T. / Liu, S. / Pang, H. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis Authors: Zheng, X.D. / Guo, J. / Xu, L. / Li, H. / Zhang, D. / Zhang, K. / Sun, F. / Wen, T. / Liu, S. / Pang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p2m.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p2m.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/3p2m ftp://data.pdbj.org/pub/pdb/validation_reports/p2/3p2m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35544.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0045c / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71702, Hydrolases |
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#2: 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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M magnesium chloride, 100 mM Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07176 / Wavelength: 1.07176 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07176 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 7159 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 80.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→38.35 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 20.082 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.88 Å / Total num. of bins used: 20
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