+Open data
-Basic information
Entry | Database: PDB / ID: 1w5d | ||||||
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Title | Crystal structure of PBP4a from Bacillus subtilis | ||||||
Components | PENICILLIN-BINDING PROTEINPenicillin-binding proteins | ||||||
Keywords | HYDROLASE / PENICILLIN-BINDING PROTEIN / D-ALA-D-ALA-CARBOXYPEPTIDASE / PEPTIDOGLYCAN / BACILLUS SUBTILIS / BETA-LACTAM / PEPTIDOGLYCAN SYNTHESIS | ||||||
Function / homology | Function and homology information serine-type carboxypeptidase activity / peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / membrane raft / cell division ...serine-type carboxypeptidase activity / peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / membrane raft / cell division / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sauvage, E. / Herman, R. / Petrella, S. / Duez, C. / Frere, J.M. / Charlier, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of the Bacillus Subtilis Penicillin-Binding Protein 4A, and its Complex with a Peptidoglycan Mimetic Peptide. Authors: Sauvage, E. / Duez, C. / Herman, R. / Kerff, F. / Petrella, S. / Anderson, J.W. / Adediran, S.A. / Pratt, R.F. / Frere, J.M. / Charlier, P. #1: Journal: J.Bacteriol. / Year: 2001 Title: Purification and Characterization of Pbp4A, a New Low-Molecular-Weight Penicillin-Binding Protein from Bacillus Subtilis Authors: Duez, C. / Vanhove, M. / Gallet, X. / Bouillenne, F. / Docquier, J.D. / Brans, A. / Frere, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w5d.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w5d.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 1w5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/1w5d ftp://data.pdbj.org/pub/pdb/validation_reports/w5/1w5d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49762.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria) References: UniProt: P39844, serine-type D-Ala-D-Ala carboxypeptidase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | pH: 7.8 / Details: TRIS 0.1M, KCL 0.8M, PH 7.8, PEG3350, CACL2 0.2M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976267 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2001 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976267 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→58.38 Å / Num. obs: 34499 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2233933.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7461 Å2 / ksol: 0.351299 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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