+Open data
-Basic information
Entry | Database: PDB / ID: 4de1 | |||||||||
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Title | CTX-M-9 class A beta-lactamase complexed with compound 18 | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | Hydrolase/hydrolase inhibitor / CTX-M / beta-lactamase / molecular docking / fragment / 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: 1.26 Å | |||||||||
Authors | Nichols, D.A. / Chen, Y. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase Authors: Nichols, D.A. / Jaishankar, P. / Larson, W. / Smith, E. / Liu, G. / Beyrouthy, R. / Bonnet, R. / Renslo, A.R. / Chen, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4de1.cif.gz | 246.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4de1.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 4de1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/4de1 ftp://data.pdbj.org/pub/pdb/validation_reports/de/4de1 | HTTPS FTP |
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-Related structure data
Related structure data | 4ddsC 4ddyC 4de0C 4de2C 4de3C 3g35S 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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2 |
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Unit cell |
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Details | The biological unit is monomer. There are 2 biological units in the asymmetric unit. |
-Components
#1: Protein | Mass: 27955.463 Da / Num. of mol.: 2 / Fragment: unp 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, blaCTX-M-9b, CTX-M / Plasmid: PET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase #2: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Potassium Phosphate, pH 8.5, vapor diffusion, hanging drop, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.67019 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.67019 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→50 Å / Num. all: 119169 / Num. obs: 118432 / % possible obs: 99.4 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.042 / Χ2: 1.077 / Net I/σ(I): 21.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3G35 Resolution: 1.26→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.237 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.11 Å2 / Biso mean: 11.4473 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.259→1.291 Å / Total num. of bins used: 20
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