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Yorodumi- PDB-5evl: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5evl | ||||||
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Title | Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å | ||||||
Authors | Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5evl.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5evl.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 5evl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5evl ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5evl | 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
#1: Protein | Mass: 40555.953 Da / Num. of mol.: 1 / Fragment: UNP residues 26-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: ampC, CV_1310 / Plasmid: pMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7NYG4, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 2.0 M Ammonium Sulfate, 0.1 M Citric Acid:NaOH, pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. all: 48204 / Num. obs: 48204 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.11 Å2 / Rsym value: 0.082 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.68 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.52→35.909 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→35.909 Å
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Refine LS restraints |
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LS refinement shell |
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