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Yorodumi- PDB-3oos: The structure of an alpha/beta fold family hydrolase from Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oos | ||||||
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Title | The structure of an alpha/beta fold family hydrolase from Bacillus anthracis str. Sterne | ||||||
Components | Alpha/beta hydrolase family protein | ||||||
Keywords | HYDROLASE / APC67239.0 / Protein Structure Initiative / PSI-2 / Structural Genomics / Midwest Center for Structural Genomics / MCSG / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / alpha/beta fold family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Fan, Y. / Tan, K. / Bigelow, L. / Hamilton, J. / Li, H. / Zhou, Y. / Clancy, S. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of an alpha/beta fold family hydrolase from Bacillus anthracis str. Sterne Authors: Fan, Y. / Tan, K. / Bigelow, L. / Hamilton, J. / Li, H. / Zhou, Y. / Clancy, S. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oos.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oos.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3oos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/3oos ftp://data.pdbj.org/pub/pdb/validation_reports/oo/3oos | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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: 31877.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2502, BA_2687, GBAA2687, GBAA_2687 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81PV7, UniProt: A0A6L8NXE0*PLUS | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium sulfate, 0.1M HEPES pH7.5, 16%w/v PEG4000, 10%w/v isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 22, 2010 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. all: 40780 / Num. obs: 40780 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 56.03 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 12 / Num. unique all: 2017 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→65.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.974 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.084 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: 16.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→65.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.655→1.698 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.3391 Å / Origin y: 21.7885 Å / Origin z: 37.2034 Å
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