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Yorodumi- PDB-4jpm: Structure of SHV-1 beta-lactamase in complex with the 7-alkyliden... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jpm | ||||||
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Title | Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / 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 / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Rodkey, E.A. / van den Akker, F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: beta-Lactamase Inhibition by 7-Alkylidenecephalosporin Sulfones: Allylic Transposition and Formation of an Unprecedented Stabilized Acyl-Enzyme. Authors: Rodkey, E.A. / McLeod, D.C. / Bethel, C.R. / Smith, K.M. / Xu, Y. / Chai, W. / Che, T. / Carey, P.R. / Bonomo, R.A. / van den Akker, F. / Buynak, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jpm.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jpm.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jpm_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4jpm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4jpm_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4jpm_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jpm ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jpm | HTTPS FTP |
-Related structure data
Related structure data | 1shvS 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: 31259.988 Da / Num. of mol.: 1 / Fragment: SVH-1 beta-lactamase 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 | ChemComp-1OG / | #4: Chemical | ChemComp-EPE / | #5: 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: 1.84 Å3/Da / Density % sol: 32.98 % |
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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: BL7-1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010 |
Radiation | Monochromator: Monochr. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→24.41 Å / Num. all: 79862 / Num. obs: 76013 / % possible obs: 95.18 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 3.2 % / Rsym value: 0.351 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1SHV Resolution: 1.14→24.41 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.018 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / 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: 15.605 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→24.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.142→1.172 Å / Total num. of bins used: 20
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