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Yorodumi- PDB-6cyu: Crystal structure of CTX-M-14 S70G/N106S/D240G beta-lactamase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cyu | ||||||
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Title | Crystal structure of CTX-M-14 S70G/N106S/D240G beta-lactamase in complex with hydrolyzed cefotaxime | ||||||
Components | Beta-lactamase | ||||||
Keywords | hydrolase/antibiotic / Beta-lactamase CTX-M-14 / hydrolase-hydrolase inhibitor complex / hydrolase-antibiotic complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Patel, M.P. / Hu, L. / Sankaran, B. / Brown, C. / Prasad, B.V.V. / Palzkill, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Synergistic effects of functionally distinct substitutions in beta-lactamase variants shed light on the evolution of bacterial drug resistance. Authors: Patel, M.P. / Hu, L. / Brown, C.A. / Sun, Z. / Adamski, C.J. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cyu.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cyu.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cyu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6cyu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6cyu_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6cyu_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cyu ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cyu | HTTPS FTP |
-Related structure data
Related structure data | 6cykC 6cynC 6cyqC 1yltS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 27885.457 Da / Num. of mol.: 1 / Mutation: S70G, N106S, D240G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, BK334_27290, BMR21_24310, BMR35_25520, BMR49_25760, BXT93_06855, CA268_29135, CDL37_21060, CR538_26855, ETN48_p0088, pCT_085, pHK01_011 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9L5C7, UniProt: Q9L5C8*PLUS, beta-lactamase |
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#2: Chemical | ChemComp-CE4 / ( |
#3: 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: 2.05 Å3/Da / Density % sol: 39.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→35.427 Å / Num. obs: 21719 / % possible obs: 99.78 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.82→1.85 Å / Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLT Resolution: 1.82→35.427 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→35.427 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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