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Yorodumi- PDB-5df9: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5df9 | ||||||
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Title | CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH DEACYLATED PRODUCT OF CEFOPERAZONE | ||||||
Components | Cell division protein | ||||||
Keywords | TRANSFERASE / cefoperazone / beta-lactam antibiotics / acyl-enzyme complex / de-acylation | ||||||
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: 2.7 Å | ||||||
Authors | Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J. | ||||||
Citation | Journal: Febs Lett. / Year: 2016 Title: Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms. Authors: Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5df9.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5df9.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 5df9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5df9_validation.pdf.gz | 752.5 KB | Display | wwPDB validaton report |
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Full document | 5df9_full_validation.pdf.gz | 755.8 KB | Display | |
Data in XML | 5df9_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 5df9_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5df9 ftp://data.pdbj.org/pub/pdb/validation_reports/df/5df9 | HTTPS FTP |
-Related structure data
Related structure data | 5df7C 5df8SC S: Starting model for refinement C: citing same article (ref.) |
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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: UNP residues 35-579 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: pbpB, ftsI_2, ERS445055_04698, PAE221_03076, YQ19_27590 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q51504, peptidoglycan glycosyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-59J / ( | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1.26 M (NH4)2SO4; 0.1 M CHES pH 9.5; 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 15866 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DF8 Resolution: 2.7→29.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 31.791 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / 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: 75.155 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→29.97 Å
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Refine LS restraints |
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