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Yorodumi- PDB-2oqz: The crystal structure of sortase B from B.anthracis in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oqz | ||||||
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Title | The crystal structure of sortase B from B.anthracis in complex with AAEK2 | ||||||
Components | Sortase B | ||||||
Keywords | HYDROLASE / sortase B 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: 1.6 Å | ||||||
Authors | Wu, R. / Zhang, R. / Maresso, 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 | 2oqz.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oqz.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 2oqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/2oqz ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oqz | HTTPS FTP |
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-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: 26991.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: BA_4783, BAS4438, GBAA4783 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q81L49, UniProt: A0A6L8PZR0*PLUS, cruzipain | ||
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#2: Chemical | #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: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M LiSO4, 19% PEG6000, pH 6.5, 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-BM / Wavelength: 0.9798 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 24, 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: 1.6→50 Å / Num. all: 28881 / Num. obs: 27707 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.78 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.72 / Num. unique all: 1315 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→42.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.563 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 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: 23.044 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.569 Å / Origin y: 28.729 Å / Origin z: 29.342 Å
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