+Open data
-Basic information
Entry | Database: PDB / ID: 6hr4 | ||||||
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Title | Apo form of penicillin-binding protein 3 from P. aeruginosa | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | PENICILLIN-BINDING PROTEIN / penicillin-binding protein peptidoglycan / Hydrolase | ||||||
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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Bellini, D. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Apo form of penicillin-binding protein 3 from P. aeruginosa Authors: Bellini, D. / Dowson, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hr4.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hr4.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hr4 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hr4 | HTTPS FTP |
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-Related structure data
Related structure data | 3oc2S 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: 57872.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: 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: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 7.8. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→82 Å / Num. obs: 120346 / % possible obs: 100 % / Redundancy: 4.7 % / Rrim(I) all: 0.054 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.19→1.21 Å / Rrim(I) all: 0.714 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3oc2 Resolution: 1.19→60.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.852 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.014 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→60.08 Å
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Refine LS restraints |
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