+Open data
-Basic information
Entry | Database: PDB / ID: 9c84 | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase with inhibitor | ||||||
Components | AmpC Beta-lactamase | ||||||
Keywords | HYDROLASE / inhibitor | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Liu, F. / Shoichet, B.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Improved correlations with score, hit-rate, and affinity as docking library and testing scale increase Authors: Liu, F. / 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 | 9c84.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c84.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9c84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/9c84 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/9c84 | HTTPS FTP |
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-Related structure data
Related structure data | 9c6pC 9c81C 9c83C 9c8jC C: citing same article (ref.) |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41593.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase #2: Chemical | Mass: 387.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9Cl2FN2O3S / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2M KPI; pH 8.56 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2023 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→58.57 Å / Num. obs: 79680 / % possible obs: 91.69 % / Redundancy: 1.99 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01791 / Net I/σ(I): 24.78 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.09036 / Mean I/σ(I) obs: 7.04 / Num. unique obs: 5027 / CC1/2: 0.977 / CC star: 0.994 / % possible all: 58.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→58.57 Å / SU ML: 0.151 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6594 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: 24.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→58.57 Å
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Refine LS restraints |
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LS refinement shell |
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