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Yorodumi- PDB-3pyw: The structure of the SLH domain from B. anthracis surface array p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pyw | ||||||
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Title | The structure of the SLH domain from B. anthracis surface array protein at 1.8A | ||||||
Components | S-layer protein sap | ||||||
Keywords | STRUCTURAL PROTEIN / SLH-domains / polysaccharide binding / GST-SLH / cell wall / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / polysaccharide / S-layer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhang, R. / Wilton, R. / Kern, J. / Joachimiak, A. / Schneewind, O. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure of Surface Layer Homology (SLH) Domains from Bacillus anthracis Surface Array Protein. Authors: Kern, J. / Wilton, R. / Zhang, R. / Binkowski, T.A. / Joachimiak, A. / Schneewind, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pyw.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pyw.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/3pyw ftp://data.pdbj.org/pub/pdb/validation_reports/py/3pyw | 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: 21916.781 Da / Num. of mol.: 1 / Fragment: SLH 1, SLH 2, and SLH 3 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: steme 34F2 / Gene: BAS0841, BA_0885, GBAA_0885, GI:49183865, sap / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49051 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 3.46 Å3/Da / Density % sol: 64.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M citrate pH5.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→54.96 Å / Num. all: 27789 / Num. obs: 27750 / % possible obs: 99.86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.83 |
Reflection shell | Resolution: 1.8→1.846 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.61 / Num. unique all: 2133 / % possible all: 98.55 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→54.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.211 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.088 / ESU R Free: 0.087 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→54.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.5995 Å / Origin y: 17.1266 Å / Origin z: 33.8102 Å
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Refinement TLS group |
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