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Open data
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Basic information
Entry | Database: PDB / ID: 3opp | ||||||
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Title | ESBL R164S mutant of SHV-1 beta-lactamase complexed with SA2-13 | ||||||
![]() | Beta-lactamase SHV-1 | ||||||
![]() | HYDROLASE / Class A beta-lactamase | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sampson, J.M. / van den Akker, F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ophC ![]() 3oplC ![]() 3oprC ![]() 1vm1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31189.875 Da / Num. of mol.: 1 / Mutation: R164S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SA2 / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K PH range: 6.6-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 21816 / Num. obs: 20746 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.213 / % possible all: 67.7 |
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Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1VM1 Resolution: 1.8→33.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.428 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R Free: 0.123 / 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: 18.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.75 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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