+Open data
-Basic information
Entry | Database: PDB / ID: 5kmt | ||||||
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Title | CTX-M9 mutant L48A | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta lactamase / ESBL | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Latallo, M.J. / Faham, S. / Kasson, P.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2017 Title: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme. Authors: Latallo, M.J. / Cortina, G.A. / Faham, S. / Nakamoto, R.K. / Kasson, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kmt.cif.gz | 215 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kmt.ent.gz | 172.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kmt_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 5kmt_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 5kmt_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 5kmt_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/5kmt ftp://data.pdbj.org/pub/pdb/validation_reports/km/5kmt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 27 - 287 / Label seq-ID: 29 - 289
NCS oper:
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-Components
#1: Protein | Mass: 30838.061 Da / Num. of mol.: 2 / Mutation: L48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9a, blaCTX-M-9, blaCTX-M-9b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5C8, beta-lactamase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-K / #4: 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: 1.9 Å3/Da / Density % sol: 35.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.2 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→77.47 Å / Num. obs: 47330 / % possible obs: 94.6 % / Redundancy: 8.1 % / Net I/σ(I): 26.8 |
-Processing
Software |
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Refinement | Resolution: 1.7→36.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.689 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.118 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.912 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→36.22 Å
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Refine LS restraints |
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