[English] 日本語
Yorodumi- PDB-7bn9: Crystal Structure of Bacillus subtilis Penicillin Binding Protein 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bn9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Bacillus subtilis Penicillin Binding Protein 3 | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | HYDROLASE / Transpeptidase / penicillin-binding protein / low-affinity / peptidoglycan | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Rao, V.A. / Lewis, R.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Cooperation between peptidoglycan transpeptidases and SEDS proteins in Bacillus subtilis cell division Authors: Sassine, J. / Rao, V.A. / Goldsmith, G. / Breukink, E. / Lewis, R.J. / Daniel, R.A. / Vollmer, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bn9.cif.gz | 296.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bn9.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bn9_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7bn9_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 7bn9_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 7bn9_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bn9 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bn9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 74020.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: pbpC, ycsM, yzsA, BSU04140 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P42971, serine-type D-Ala-D-Ala carboxypeptidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES, pH 7.0, 20 % (w/v) PEG 6000, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→49.46 Å / Num. obs: 42319 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 59.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.65→9.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4375 / CC1/2: 0.639 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VQQ, 3EQU Resolution: 2.65→49.46 Å / SU ML: 0.3984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9362 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→49.46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|