+Open data
-Basic information
Entry | Database: PDB / ID: 7uon | ||||||
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Title | CTX-M-14 Y105W mutant | ||||||
Components | Beta-lactamase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / beta-lactamase | ||||||
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: 1.35 Å | ||||||
Authors | Judge, A. / Hu, L. / Sankaran, B. / Van Riper, J. / Prasad, B.V.V. / Palzkill, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M beta-lactamase. Authors: Judge, A. / Hu, L. / Sankaran, B. / Van Riper, J. / Venkataram Prasad, B.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 | 7uon.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uon.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 7uon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uon_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 7uon_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 7uon_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7uon_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/7uon ftp://data.pdbj.org/pub/pdb/validation_reports/uo/7uon | HTTPS FTP |
-Related structure data
Related structure data | 1yltS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28023.582 Da / Num. of mol.: 1 / Mutation: Y105W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0, beta-lactamase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.68 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES (0.1M), PEG 4,000 (25% w/v) |
-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: 1.00001 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2021 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→28.32 Å / Num. obs: 51539 / % possible obs: 99.1 % / Redundancy: 12.3 % / Biso Wilson estimate: 16.42 Å2 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7337 / CC1/2: 0.961 / Rpim(I) all: 0.173 / Rrim(I) all: 0.58 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLT Resolution: 1.35→28.32 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1262 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: 29.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→28.32 Å
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Refine LS restraints |
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LS refinement shell |
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