+Open data
-Basic information
Entry | Database: PDB / ID: 4bjp | ||||||
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Title | Crystal structure of E. coli penicillin binding protein 3 | ||||||
Components | PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Beta-Lactamase - #330 / Beta-Lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sauvage, E. / Joris, M. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal Structure of Penicillin-Binding Protein 3 (Pbp3) from Escherichia Coli. Authors: Sauvage, E. / Derouaux, A. / Fraipont, C. / Joris, M. / Herman, R. / Rocaboy, M. / Schloesser, M. / Dumas, J. / Kerff, F. / Nguyen-Disteche, M. / Charlier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bjp.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bjp.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bjp ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bjp | HTTPS FTP |
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-Related structure data
Related structure data | 4bjqC 3equS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55378.129 Da / Num. of mol.: 1 / Fragment: RESIDUES 67-577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: J2XFH0, peptidoglycan glycosyltransferase |
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-Non-polymers , 6 types, 164 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97628 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→82.7 Å / Num. obs: 20753 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EQU Resolution: 2.5→59.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.026 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→59.51 Å
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Refine LS restraints |
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