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Yorodumi- PDB-4kqo: Crystal structure of penicillin-binding protein 3 from pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kqo | ||||||
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Title | Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | Biosynthetic Protein/Antibiotic / PENICILLIN-BINDING PROTEINS / PIPERACILLIN / CELL WALL BIOSYNTHESIS / TRANSPEPTIDASE / OUT PERIPLASMIC MEMBRANE / Biosynthetic Protein-Antibiotic complex | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Nettleship, J.E. / Stuart, D.I. / Owens, R.J. / Ren, J. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Binding of (5S)-Penicilloic Acid to Penicillin Binding Protein 3. Authors: van Berkel, S.S. / Nettleship, J.E. / Leung, I.K. / Brem, J. / Choi, H. / Stuart, D.I. / Claridge, T.D. / McDonough, M.A. / Owens, R.J. / Ren, J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kqo.cif.gz | 396.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kqo.ent.gz | 322.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kqo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4kqo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4kqo_validation.xml.gz | 40 KB | Display | |
Data in CIF | 4kqo_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kqo ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kqo | HTTPS FTP |
-Related structure data
Related structure data | 4kqqC 4kqrC 3oclS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 58 - 562 / Label seq-ID: 43 - 547
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61152.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ftsI, PA4418 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XD46 |
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-Non-polymers , 5 types, 284 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IMD / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.5 M NaCl; 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 55461 / % possible obs: 97.8 % / Observed criterion σ(I): -1.5 / Redundancy: 9.4 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4929 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OCL Resolution: 2.31→47.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.914 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.231 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.412 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→47.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 29717 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.31→2.37 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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