[English] 日本語
Yorodumi- PDB-2waf: PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2waf | ||||||
---|---|---|---|---|---|---|---|
Title | PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6) | ||||||
Components | PENICILLIN-BINDING PROTEIN 2B | ||||||
Keywords | PEPTIDE BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / TRANSMEMBRANE / ANTIBIOTIC RESISTANCE / CELL SHAPE / PEPTIDOGLYCAN / CELL MEMBRANE / CELL WALL BIOGENESIS/DEGRADATION / MEMBRANE / INFECTION / RESISTANCE / ANTIBIOTIC | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å | ||||||
Authors | Contreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Pbp Active Site Flexibility as the Key Mechanism for Beta-Lactam Resistance in Pneumococci Authors: Contreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A. #1: Journal: Antimicrob.Agents Chemother. / Year: 2004 Title: Biochemical Characterization of Streptococcus Pneumoniae Penicillin-Binding Protein 2B and its Implication in Beta-Lactam Resistance Authors: Pagliero, E. / Chesnel, L. / Hopkins, J. / Croize, J. / Dideberg, O. / Vernet, T. / Di-Guilmi, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2waf.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2waf.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 2waf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2waf ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2waf | HTTPS FTP |
---|
-Related structure data
Related structure data | 2wadSC 2waeC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 74210.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 References: UniProt: P0A3M6, Hydrolases; Acting on peptide bonds (peptidases) | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.65 % / Description: NONE |
---|---|
Crystal grow | pH: 8 / Details: 1.4M (NH4)2SO4, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9312 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 9, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9312 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→47.25 Å / Num. obs: 14291 / % possible obs: 82.5 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 69.16 Å2 / Rsym value: 0.1 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.29→3.49 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.82 / Rsym value: 0.44 / % possible all: 54.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WAD Resolution: 3.29→47.25 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.867 / SU B: 78.151 / SU ML: 0.532 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / 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: 91.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→47.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|