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Yorodumi- PDB-6v8v: Crystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v8v | ||||||
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Title | Crystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase in complex with ceftazidime-2 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / drug resistance / protein evolution / conformational change / enzyme kinetics / enzyme catalysis / protein stability / protein-drug interaction | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Brown, C.A. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Antagonism between substitutions in beta-lactamase explains a path not taken in the evolution of bacterial drug resistance. Authors: Brown, C.A. / Hu, L. / Sun, Z. / Patel, M.P. / Singh, S. / Porter, J.R. / Sankaran, B. / Prasad, B.V.V. / Bowman, G.R. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v8v.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v8v.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8v ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8v | HTTPS FTP |
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-Related structure data
Related structure data | 6v5eC 6v6gC 6v6pC 6v7tC 6v83C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27761.279 Da / Num. of mol.: 1 / Mutation: E166A, P167S, 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, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BET08_34355, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON66_01305, BON69_22545, BON71_04040, BON75_10525, BON76_14325, BON81_01055, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BXT93_06855, C5N07_28500, C5P43_21980, CDL37_21060, CR538_26855, CRT46_23505, DW236_20870, EIA08_25160, EIA21_26975, ELT23_05930, ETN48_p0088, FNJ69_13810, FQR64_24895, FTV90_03295, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4370290_00046 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C7, beta-lactamase |
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#2: Chemical | ChemComp-CAZ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M PCB buffer pH 6, 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00008 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00008 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.42 Å / Num. obs: 21924 / % possible obs: 97.91 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.063 / Rrim(I) all: 0.107 / Net I/σ(I): 11.72 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 4.81 / Num. unique obs: 916 / Rpim(I) all: 0.109 / Rrim(I) all: 0.158 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLT Resolution: 1.8→32.44 Å / SU ML: 0.146 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.5644 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→32.44 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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