+Open data
-Basic information
Entry | Database: PDB / ID: 3pbt | ||||||
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Title | Crystal structure of PBP3 complexed with MC-1 | ||||||
Components | Penicillin-binding protein 3 | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / PBP3 / HYDROLASE-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: 1.641 Å | ||||||
Authors | Han, S. / Evdokimov, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa. Authors: Han, S. / Zaniewski, R.P. / Marr, E.S. / Lacey, B.M. / Tomaras, A.P. / Evdokimov, A. / Miller, J.R. / Shanmugasundaram, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pbt.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbt.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbt ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbt | 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
#1: Protein | Mass: 58329.453 Da / Num. of mol.: 1 / Fragment: UNP Residues 50-579 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ftsI, PA4418, pbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q51504, UniProt: G3XD46*PLUS |
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#2: Chemical | ChemComp-UE1 / ( |
#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: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M citrate, 30% PEG3350, 0.3M Mg(NO3)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→61.12 Å / Num. obs: 62097 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.641→61.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.788 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / 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: 22.645 Å2
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Refinement step | Cycle: LAST / Resolution: 1.641→61.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.641→1.684 Å / Total num. of bins used: 20
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