[English] 日本語
Yorodumi- PDB-5evi: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5evi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae | ||||||
Components | (Beta-Lactamase/D-Alanine ...) x 4 | ||||||
Keywords | HYDROLASE / alpha-beta-fold / Structural Genomics / PSI-Biology / 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 | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5evi.cif.gz | 526.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5evi.ent.gz | 451.9 KB | Display | PDB format |
PDBx/mmJSON format | 5evi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5evi_validation.pdf.gz | 492.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5evi_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | 5evi_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 5evi_validation.cif.gz | 77.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5evi ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5evi | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Beta-Lactamase/D-Alanine ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 40686.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase |
---|---|
#2: Protein | Mass: 40686.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase |
#3: Protein | Mass: 40686.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase |
#4: Protein | Mass: 40713.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: DC3000 / Gene: ampC, PSPTO_3594 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q87Z37, beta-lactamase |
-Non-polymers , 3 types, 523 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.95 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å | |||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015 | |||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
| |||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 128402 / Num. obs: 128402 / % possible obs: 97.5 % / Redundancy: 2.2 % / Rsym value: 0.054 / Net I/σ(I): 12.44 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.49 / % possible all: 96.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.753 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.853 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|