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- PDB-3w4o: Crystal structure of PenI beta-lactamase from Burkholderia pseudo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w4o | ||||||
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Title | Crystal structure of PenI beta-lactamase from Burkholderia pseudomallei at pH9.5 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / beta-Lactamase | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nukaga, M. / Ohuchi, N. / Papp-Wallace, K.M. / Taracila, M.A. / Bonomo, R.A. | ||||||
![]() | ![]() Title: Insights into beta-lactamases from Burkholderia species, two phylogenetically related yet distinct resistance determinants Authors: Papp-Wallace, K.M. / Taracila, M.A. / Gatta, J.A. / Ohuchi, N. / Bonomo, R.A. / Nukaga, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3w4pC ![]() 3w4qC ![]() 2p74S 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: 28383.168 Da / Num. of mol.: 1 / Fragment: UNP residues 31-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NHE / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 25% PEG8000, 0.1M CHESS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 68591 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.04 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2p74 Resolution: 1.18→15 Å / Num. parameters: 22240 / Num. restraintsaints: 28349 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 10.68 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 28 / Occupancy sum hydrogen: 1939 / Occupancy sum non hydrogen: 2320.23 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→15 Å
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Refine LS restraints |
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