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Yorodumi- PDB-6i1f: Crystal structure of TP domain from Chlamydia trachomatis Penicil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i1f | ||||||
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Title | Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with amoxicillin | ||||||
Components | Penicillin-binding protein,Penicillin-binding protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with amoxicillin Authors: Bellini, D. / Koekemoer, L. / Newman, H. / 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 | 6i1f.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i1f.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 6i1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i1f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6i1f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6i1f_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6i1f_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i1f ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i1f | HTTPS FTP |
-Related structure data
Related structure data | 6hzhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36467.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: pbp_2, ERS133248_00492 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0E9FXJ8, peptidoglycan glycosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1 M sodium citrate and 0.1 M sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
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: 1.9→91.99 Å / Num. obs: 42354 / % possible obs: 93.4 % / Redundancy: 12.1 % / Rrim(I) all: 0.283 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.9→2.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HZH Resolution: 1.89→91.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.514 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.194 / 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: 27.072 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→91.99 Å
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Refine LS restraints |
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