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Yorodumi- PDB-2oqw: The crystal structure of sortase B from B.anthracis in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oqw | ||||||
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Title | The crystal structure of sortase B from B.anthracis in complex with AAEK1 | ||||||
Components | Sortase B | ||||||
Keywords | HYDROLASE / SortaseB protein / inhibitor / B. anthracis / the Great Lakes Regional Center of Excellence / GLRCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Wu, R. / Zhang, R. / Marresso, A.W. / Schneewind, O. / Joachimiak, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Activation of inhibitors by sortase triggers irreversible modification of the active site. Authors: Maresso, A.W. / Wu, R. / Kern, J.W. / Zhang, R. / Janik, D. / Missiakas, D.M. / Duban, M.E. / 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 | 2oqw.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oqw.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 2oqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oqw_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 2oqw_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 2oqw_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2oqw_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/2oqw ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oqw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | this protein exists as a monomer |
-Components
#1: Protein | Mass: 26928.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Strain: Ames / Gene: BA_4783, BAS4438, GBAA4783 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81L49, UniProt: A0A6L8PZR0*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | THE E.C. NUMBER FOR THIS PROTEIN IS 3.4.22.B51 ACCORDING TO BRENDA ENZYME INFORMATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M MgCl2, 25% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 315 / Detector: CCD / Date: Apr 5, 2006 / 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: 2→50 Å / Num. obs: 14492 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.95 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.87 / Num. unique all: 1119 / % possible all: 72.33 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.945 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.211 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: 34.175 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.9762 Å / Origin y: 5.4348 Å / Origin z: 11.7745 Å
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