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Yorodumi- PDB-5ee8: Crystal structure of S02030 boronic acid inhibitor complexed to S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ee8 | ||||||
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Title | Crystal structure of S02030 boronic acid inhibitor complexed to SHV-1 beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / transition state inhibitor / 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 | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Krishnan, N. / van den Akker, F. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2016 Title: Crystal Structures of KPC-2 and SHV-1 beta-Lactamases in Complex with the Boronic Acid Transition State Analog S02030. Authors: Nguyen, N.Q. / Krishnan, N.P. / Rojas, L.J. / Prati, F. / Caselli, E. / Romagnoli, C. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ee8.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ee8.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ee8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5ee8 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5ee8 | HTTPS FTP |
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-Related structure data
Related structure data | 5eecC 2h5sS 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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Unit cell |
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-Components
#1: Protein | Mass: 28907.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AD64, beta-lactamase | ||
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#2: Chemical | ChemComp-ZXM / | ||
#3: Chemical | #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: 1.98 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20-30% PEG 6000, 100mM Tris pH 7.5, 0.56mM cymal-6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: 1.1271 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→50 Å / Num. obs: 33737 / % possible obs: 97 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Χ2: 1.051 / Net I/av σ(I): 16.548 / Net I/σ(I): 10.7 / Num. measured all: 122260 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H5S Resolution: 1.54→33.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.354 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.42 Å2 / Biso mean: 15.141 Å2 / Biso min: 8.15 Å2
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Refinement step | Cycle: final / Resolution: 1.54→33.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.538→1.578 Å / Total num. of bins used: 20
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