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Yorodumi- PDB-3lac: Crystal structure of Bacillus anthracis pyrrolidone-carboxylate p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lac | ||||||
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Title | Crystal structure of Bacillus anthracis pyrrolidone-carboxylate peptidase, pcP | ||||||
Components | Pyrrolidone-carboxylate peptidase | ||||||
Keywords | HYDROLASE / alpha beta class / three layer sandwich / Bacillus anthracis / CSGID / Protease / Thiol protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Bacillus anthracis pyrrolidone-carboxylate peptidase, pcP Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lac.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lac.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lac_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 3lac_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 3lac_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3lac_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/3lac ftp://data.pdbj.org/pub/pdb/validation_reports/la/3lac | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23788.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: pcp, BA_3090, GBAA_3090, BAS2875 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81NT5, pyroglutamyl-peptidase I #2: Chemical | ChemComp-PEG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 3350, 1% PEG 5KMME, 200mM magnesium chloride, 100mM Tris pH 8.5, 0.5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2009 / Details: beryllium lens |
Radiation | Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.3 Å / Num. all: 30826 / Num. obs: 30518 / % possible obs: 99 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3 / Num. unique all: 3040 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→34.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 8.287 / SU ML: 0.107 / SU R Cruickshank DPI: 0.18 / SU Rfree: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 91.65 Å2 / Biso mean: 16.685 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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