+Open data
-Basic information
Entry | Database: PDB / ID: 1ylt | |||||||||
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Title | Atomic resolution structure of CTX-M-14 beta-lactamase | |||||||||
Components | beta-lactamase CTX-M-14 | |||||||||
Keywords | HYDROLASE / CTX-M / beta-lactamase / anisotropy / extended-spectrum | |||||||||
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 / AB INITIO / Resolution: 1.1 Å | |||||||||
Authors | Chen, Y. / Delmas, J. / Sirot, J. / Shoichet, B. / Bonnet, R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Atomic Resolution Structures of CTX-M beta-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability. Authors: Chen, Y. / Delmas, J. / Sirot, J. / Shoichet, B. / Bonnet, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ylt.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ylt.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ylt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ylt_validation.pdf.gz | 817.7 KB | Display | wwPDB validaton report |
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Full document | 1ylt_full_validation.pdf.gz | 822.8 KB | Display | |
Data in XML | 1ylt_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1ylt_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1ylt ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1ylt | HTTPS FTP |
-Related structure data
Related structure data | 1yljSC 1ylpC 1ylwC S: Starting model for refinement C: citing same article (ref.) |
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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: 28000.547 Da / Num. of mol.: 1 / Mutation: A231V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M / Plasmid: pET-9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: CTX-M-14 beta-lactamase / References: UniProt: Q9L5C7, beta-lactamase | ||
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 1.72 Å3/Da / Density % sol: 28.4 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.033 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2004 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→22 Å / Num. obs: 89046 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.23 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.02 / % possible all: 76.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1YLJ Resolution: 1.1→22 Å / Num. parameters: 23478 / Num. restraintsaints: 32095 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT. RIDING HYDROGENS INCLUDED IN REFINEMENT. WATER MOLECULES IN CLOSE CONTACT HAVE A COMBINED OCCUPANCY OF 1.
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Refine analyze | Num. disordered residues: 122 / Occupancy sum hydrogen: 1886 / Occupancy sum non hydrogen: 2391.66 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→22 Å
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Refine LS restraints |
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