+Open data
-Basic information
Entry | Database: PDB / ID: 3opl | ||||||
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Title | ESBL R164H mutant SHV-1 beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / Class A beta-lactamase | ||||||
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: 1.8 Å | ||||||
Authors | Sampson, J.M. / van den Akker, F. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2011 Title: Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase. Authors: Sampson, J.M. / Ke, W. / Bethel, C.R. / Pagadala, S.R. / Nottingham, M.D. / Bonomo, R.A. / Buynak, J.D. / 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 | 3opl.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3opl.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3opl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3opl_validation.pdf.gz | 886.9 KB | Display | wwPDB validaton report |
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Full document | 3opl_full_validation.pdf.gz | 885.1 KB | Display | |
Data in XML | 3opl_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3opl_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/3opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/3opl | HTTPS FTP |
-Related structure data
Related structure data | 3ophC 3oppC 3oprC 1vm1S 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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Details | monomer in asymmetric unit |
-Components
#1: Protein | Mass: 31240.945 Da / Num. of mol.: 1 / Mutation: R164H 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-EPE / | #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: 1.83 Å3/Da / Density % sol: 32.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K PH range: 6.6-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2006 |
Radiation | Monochromator: a vertically focusing mirror and a horizontally focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 21910 / Num. obs: 19477 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2 / % possible all: 70.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1VM1 Resolution: 1.8→42.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.53 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / 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: 27.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→42.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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