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Open data
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Basic information
Entry | Database: PDB / ID: 2oe9 | ||||||
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Title | High-pressure structure of pseudo-WT T4 Lysozyme | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / High-pressure / T4 Lysozyme | ||||||
Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Collins, M.D. / Quillin, M.L. / Matthews, B.W. / Gruner, S.M. | ||||||
![]() | ![]() Title: Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography. Authors: Collins, M.D. / Quillin, M.L. / Hummer, G. / Matthews, B.W. / Gruner, S.M. #1: ![]() Title: Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation Authors: Collins, M.D. / Quillin, M.L. / Hummer, G. / Matthews, B.M. / Gruner, S.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 | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 35.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b6tC ![]() 2oe7C ![]() 2oeaC ![]() 1l63S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18628.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species (production host): Enterobacteria phage T4 sensu lato Production host: ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: ~2.0 M NA/K PHOSPHATES, 50 MM BETA-MERCAPTOETHANOL, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si xtal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→60 Å / Num. obs: 12985 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Χ2: 2.017 / Net I/σ(I): 23.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: pdb entry 1L63 Resolution: 2.01→52.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.155 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.995 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→52.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.067 Å / Total num. of bins used: 20
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