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Yorodumi- PDB-3ocn: Crystal structure of penicillin-binding protein 3 from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ocn | ||||||
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Title | Crystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa in complex with ceftazidime | ||||||
Components | penicillin-binding protein 3 | ||||||
Keywords | PENICILLIN-BINDING PROTEIN/ANTIBIOTIC / penicillin-binding proteins / Pseudomonas aeruginosa / ceftazidime / Structural Genomics / Oxford Protein Production Facility / OPPF / transpeptidase / cell wall biosynthesis / out periplasmic membrane / PENICILLIN-BINDING 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: 2.61 Å | ||||||
Authors | Sainsbury, S. / Bird, L. / Stuart, D.I. / Owens, R.J. / Ren, J. / Oxford Protein Production Facility (OPPF) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal structures of penicillin-binding protein 3 from Pseudomonas aeruginosa: comparison of native and antibiotic-bound forms Authors: Sainsbury, S. / Bird, L. / Rao, V. / Shepherd, S.M. / Stuart, D.I. / Hunter, W.N. / Owens, R.J. / Ren, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ocn.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ocn.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 3ocn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ocn_validation.pdf.gz | 784.7 KB | Display | wwPDB validaton report |
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Full document | 3ocn_full_validation.pdf.gz | 790.9 KB | Display | |
Data in XML | 3ocn_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 3ocn_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3ocn ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3ocn | HTTPS FTP |
-Related structure data
Related structure data | 3oc2C 3oclSC 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
#1: Protein | Mass: 61152.590 Da / Num. of mol.: 1 / Fragment: residues in UNP 35-579 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4418 / Plasmid: OPPF6502 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q51504 |
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#2: Chemical | ChemComp-CTJ / |
#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: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 15047 / % possible obs: 98.6 % / Observed criterion σ(I): -1.5 / Redundancy: 5.6 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1331 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OCL Resolution: 2.61→29.85 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.68 / SU ML: 0.202 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 32.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.607→2.674 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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