+Open data
-Basic information
Entry | Database: PDB / ID: 3pbn | ||||||
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Title | Crystal Structure of Apo PBP3 from Pseudomonas aeruginosa | ||||||
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: 2 Å | ||||||
Authors | Han, S. | ||||||
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 | 3pbn.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbn.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 3pbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbn ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbn | 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: 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: 1.84 Å3/Da / Density % sol: 33.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.2M MgCl2, 0.1M Tis, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: 2→60 Å / Num. all: 63021 / Num. obs: 29054 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 28.71 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.54 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.8952 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.191 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.17 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.235 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 15
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