+Open data
-Basic information
Entry | Database: PDB / ID: 7ti0 | ||||||
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Title | Structure of CTX-M-15 bound to RPX-7063 at 1.5A | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / CTX-M-15 / ANTIBIOTIC | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Clifton, M.C. / Abendroth, J. / Hecker, S.J. / Edwards, T.E. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2022 Title: Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability. Authors: Reddy, K.R. / Totrov, M. / Lomovskaya, O. / Griffith, D.C. / Tarazi, Z. / Clifton, M.C. / Hecker, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ti0.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ti0.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ti0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ti0_validation.pdf.gz | 765.6 KB | Display | wwPDB validaton report |
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Full document | 7ti0_full_validation.pdf.gz | 765.6 KB | Display | |
Data in XML | 7ti0_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 7ti0_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/7ti0 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/7ti0 | HTTPS FTP |
-Related structure data
Related structure data | 7ti1C 7ti2C 1ymsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28138.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: blaCTX-M-15, bla_1, bla_10, bla_2, bla_3, blaCTX-M, CTX-M, CTX-M-15, ctx-m-15 Production host: Escherichia coli (E. coli) / References: UniProt: Q2PUH3, beta-lactamase |
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-Non-polymers , 5 types, 298 molecules
#2: Chemical | ChemComp-ZXQ / {( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M bis-tris propane pH 7.0, 2.3M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 39211 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.97 % / Biso Wilson estimate: 12.638 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 18.79 / Net I/σ(I): 18.79 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1yms Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.975 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 7.305 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 45.4793 Å / Origin y: 38.8027 Å / Origin z: 12.2183 Å
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