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- PDB-5xpf: High-resolution X-ray structure of the T26H mutant of T4 lysozyme -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xpf | |||||||||
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Title | High-resolution X-ray structure of the T26H mutant of T4 lysozyme | |||||||||
![]() | Endolysin | |||||||||
![]() | HYDROLASE / Alpha and beta protein / T26H mutant / Perdeuterated protein | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Hiromoto, T. / Kuroki, R. | |||||||||
![]() | ![]() Title: Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type. Authors: Hiromoto, T. / Meilleur, F. / Shimizu, R. / Shibazaki, C. / Adachi, M. / Tamada, T. / Kuroki, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xpeC ![]() 1qt8S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18665.406 Da / Num. of mol.: 1 / Mutation: T26H, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 257 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-HEZ / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sodium-potassium phosphate, Sodium chloride, 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2014 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 95774 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.019 / Rrim(I) all: 0.045 / Rsym value: 0.041 / Χ2: 2.263 / Net I/av σ(I): 51.6 / Net I/σ(I): 51.6 |
Reflection shell | Resolution: 1.04→1.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 9481 / CC1/2: 0.886 / Rpim(I) all: 0.215 / Rrim(I) all: 0.422 / Rsym value: 0.361 / Χ2: 1.732 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QT8 Resolution: 1.04→45.58 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
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Displacement parameters | Biso max: 96.95 Å2 / Biso mean: 18.1199 Å2 / Biso min: 7.69 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.04→45.58 Å
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Refine LS restraints |
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