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Yorodumi- PDB-5eec: Crystal structure of KPC-2 beta-lactamase in complex with the S02... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eec | ||||||
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Title | Crystal structure of KPC-2 beta-lactamase in complex with the S02030 boronic acid inhibitor | ||||||
Components | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
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 / Resolution: 1.87 Å | ||||||
Authors | Nguyen, N.Q. / 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 | 5eec.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eec.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eec_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5eec_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5eec_validation.xml.gz | 26 KB | Display | |
Data in CIF | 5eec_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5eec ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5eec | HTTPS FTP |
-Related 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: 28504.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F663, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% PEG 8000, 0.2 M lithium sulfate, and 0.1 M sodium acetate (pH 4.5) and 10:1 molar ratio with S02030 inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 22, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 39177 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.107 / Χ2: 1.179 / Net I/av σ(I): 9.005 / Net I/σ(I): 9.7 / Num. measured all: 113565 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.87→32.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.211 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.138 / 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: 500 Å2 / Biso mean: 13.044 Å2 / Biso min: 2.95 Å2
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Refinement step | Cycle: final / Resolution: 1.87→32.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.866→1.915 Å / Total num. of bins used: 20
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