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Yorodumi- PDB-4mbf: Crystal structure of Penam sulfone PSR-4-157 bound to SHV-1 beta-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mbf | ||||||
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Title | Crystal structure of Penam sulfone PSR-4-157 bound to SHV-1 beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | hydrolase/hydrolase inhibitor / Class A beta-lactamase / hydrolase / 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 / FOURIER SYNTHESIS / Resolution: 1.54 Å | ||||||
Authors | Rodkey, E.A. / van den Akker, F. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Penam sulfones and beta-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition. Authors: Rodkey, E.A. / Winkler, M.L. / Bethel, C.R. / Pagadala, S.R. / Buynak, J.D. / 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 | 4mbf.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mbf.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mbf_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4mbf_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4mbf_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4mbf_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/4mbf ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mbf | HTTPS FTP |
-Related 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 / Fragment: unp residues 22-286 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 | #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: 1.99 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21-30% PEG 6000, 0.1M HEPES buffer, 0.56mM Cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 6.8-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→27.71 Å / Num. all: 33044 / Num. obs: 32086 / % possible obs: 97.12 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.54→1.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.6 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.54→27.71 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.517 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→27.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20
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