[English] 日本語
Yorodumi- PDB-5ngg: Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ngg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion | ||||||
Components | Blr6230 protein | ||||||
Keywords | HYDROLASE / metallo-beta-lactamase / B3 acetate / BJP-1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bradyrhizobium diazoefficiens USDA 110 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S. | ||||||
Citation | Journal: Inorg.Chim.Acta. / Year: 2017 Title: Boric acid and acetate anion binding to subclass B3 metallo-Beta-lactamase BJP-1 provides clues for mechanism of action and inhibitor design Authors: Di Pisa, F. / Pozzi, C. / Benvenuti, M. / Docquier, J.-D. / De Luca, F. / Mangani, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ngg.cif.gz | 238.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ngg.ent.gz | 190.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ngg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ngg_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ngg_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 5ngg_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5ngg_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngg ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngg | HTTPS FTP |
-Related structure data
Related structure data | 5njwC 3lvzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31982.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria) Gene: blr6230 / Plasmid: pET-BJP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89GW5 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.38 % / Description: Clusters of parallelepiped-shaped crystals |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: BJP-1 (10 mg mL-1 in 0.1 M Tris-HCl pH 8.5 and 5 mM zinc(II) chloride) mixed with precipitant (0.2 M lithium sulfate, 30-35 % PEG4000, 0.5 M sodium acetate pH 8.5) Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→34.68 Å / Num. obs: 148959 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 6.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.18→1.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3 / Num. unique obs: 21301 / CC1/2: 0.806 / % possible all: 92.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LVZ Resolution: 1.18→34.68 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Rfactor Rfree error: 0.03 / SU B: 0.888 / SU ML: 0.02 / SU R Cruickshank DPI: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / SU Rfree Cruickshank DPI: 0.0336 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.912 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.18→34.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|