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Open data
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Basic information
Entry | Database: PDB / ID: 3g30 | ||||||
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Title | CTX-M-9 class A beta-lactamase complexed with compound 3 (G30) | ||||||
![]() | Beta-lactamase CTX-M-9a | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / Hydrolase / Plasmid / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Shoichet, B.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.4 KB | Display | ![]() |
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PDB format | ![]() | 49.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3g2yC ![]() 3g2zC ![]() 3g31C ![]() 3g32C ![]() 3g34C ![]() 3g35C ![]() 1yljS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27972.494 Da / Num. of mol.: 1 / Fragment: sequence database residues 29-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.83 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→50 Å / Num. obs: 22863 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.039 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YLJ Resolution: 1.8→38.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.811 / SU B: 3.438 / SU ML: 0.107 / SU R Cruickshank DPI: 0.158 / SU Rfree: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.143 / 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: 57.11 Å2 / Biso mean: 25.36 Å2 / Biso min: 7.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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