+Open data
-Basic information
Entry | Database: PDB / ID: 4fd8 | ||||||
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Title | Structure of apo S70C SHV beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / class A beta-lactamase / 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 / MIR / Resolution: 1.52 Å | ||||||
Authors | Rodkey, E.A. / van den Akker, F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Crystal structure of a pre-acylation complex of the beta-lactamase inhibitor, sulbactam, bound to a sulfenamide bond containing thiol-beta-lactamase Authors: Rodkey, E.A. / Drawz, S.M. / Sampson, J.M. / Bethel, C.R. / 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 | 4fd8.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fd8.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fd8_validation.pdf.gz | 681.6 KB | Display | wwPDB validaton report |
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Full document | 4fd8_full_validation.pdf.gz | 683.4 KB | Display | |
Data in XML | 4fd8_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4fd8_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fd8 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fd8 | 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: 28923.084 Da / Num. of mol.: 1 / Fragment: unp residues 22-286 / Mutation: S70C 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: 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: 2 Å3/Da / Density % sol: 38.55 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 21-30% PEG6k, 0.1M hepes pH 6.8-7.8, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K 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: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 13, 2009 |
Radiation | Monochromator: Double crystal monochromator, Rh coated flat mirror, toroidal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. all: 36725 / Num. obs: 35770 / % possible obs: 97.4 % / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.52→27.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.402 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / 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: 18.152 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→27.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.516→1.555 Å / Total num. of bins used: 20
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