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Yorodumi- PDB-3rju: Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rju | ||||||
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Title | Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate | ||||||
Components | Beta-lactamase/D-alanine Carboxypeptidase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / 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 | 3rju.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rju.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rju_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 3rju_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 3rju_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3rju_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/3rju ftp://data.pdbj.org/pub/pdb/validation_reports/rj/3rju | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38654.438 Da / Num. of mol.: 1 / Fragment: UNP residues 39-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ampH, y2964, YPO1224, YP_0915 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7CHA2, UniProt: A0A3N4B7V6*PLUS | ||
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#2: Chemical | ChemComp-CIT / | ||
#3: Chemical | #4: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.04 M potassium phosphate, 16 % w/v PEG 8000, 20 % v/v Glycerol, pH 7.5, 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-BM / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 57320 / Num. obs: 57320 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.48 Å2 / Rsym value: 0.1 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2041 / Rsym value: 0.615 / % possible all: 69.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→30.507 Å / SU ML: 0.37 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.09 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.299 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.507 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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