+Open data
-Basic information
Entry | Database: PDB / ID: 3g35 | ||||||
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Title | CTX-M-9 class A beta-lactamase complexed with compound 12 (F13) | ||||||
Components | Beta-lactamase CTX-M-9a | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / Hydrolase / Plasmid / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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: 1.41 Å | ||||||
Authors | Chen, Y. / Shoichet, B.K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2009 Title: Molecular docking and ligand specificity in fragment-based inhibitor discovery Authors: Chen, Y. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g35.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g35.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g35 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g35 | HTTPS FTP |
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-Related structure data
Related structure data | 3g2yC 3g2zC 3g30C 3g31C 3g32C 3g34C 1yljS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27972.494 Da / Num. of mol.: 2 / Fragment: sequence database residues 29-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, CTX-M / Plasmid: PET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase #2: Chemical | ChemComp-F13 / #3: Chemical | #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: 2.04 Å3/Da / Density % sol: 39.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.41→50 Å / Num. obs: 84626 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Χ2: 1.024 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YLJ Resolution: 1.41→35.36 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.903 / SU B: 1.991 / SU ML: 0.036 / SU R Cruickshank DPI: 0.079 / SU Rfree: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.73 Å2 / Biso mean: 16.826 Å2 / Biso min: 8.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→35.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.41→1.447 Å / Total num. of bins used: 20
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