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- PDB-6i1i: Crystal structure of TP domain from Escherichia coli penicillin-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i1i | ||||||
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Title | Crystal structure of TP domain from Escherichia coli penicillin-binding protein 3 in complex with penicillin | ||||||
![]() | Peptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI | ||||||
![]() | PEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance. Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.3 KB | Display | ![]() |
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Full document | ![]() | 762.5 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hzjC ![]() 6hzoC ![]() 6hzqC ![]() 6hzrC ![]() 6i1eC ![]() 6r3xC ![]() 6r40C ![]() 6r42C ![]() 4bjpS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37129.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AD69, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-JPP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20% PEG 6,000, 0.1 M CaCl2, 15% ethylene glycol and 0.1 M TrisHCl pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.25 Å / Num. obs: 32743 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rrim(I) all: 0.204 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.75→1.78 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BJP Resolution: 1.75→43.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.286 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.349 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→43.25 Å
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Refine LS restraints |
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