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Open data
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Basic information
Entry | Database: PDB / ID: 5kgr | ||||||
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Title | Spin-Labeled T4 Lysozyme Construct I9V1/V131V1 (30 days) | ||||||
![]() | Endolysin | ||||||
![]() | HYDROLASE / Spin label / EPR / DEER | ||||||
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 | ![]() ![]() | ||||||
![]() | Balo, A.R. / Feyrer, H. / Ernst, O.P. | ||||||
![]() | ![]() Title: Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains. Authors: Balo, A.R. / Feyrer, H. / Ernst, O.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
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PDB format | ![]() | 38.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452 KB | Display | ![]() |
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Full document | ![]() | 452.8 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jgnC ![]() 5jgrC ![]() 5jguC ![]() 5jgvC ![]() 5jgxC ![]() 5jgzC ![]() 1c6tS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18622.359 Da / Num. of mol.: 1 / Mutation: I9C, C54T, C97A, V131C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 282 molecules ![](data/chem/img/V1A.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-HEZ / | #4: Chemical | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2 M sodium/potassium phosphate, 150 mM sodium chloride, 100 mM 1,2-hexanediol, 3% 2-propanol PH range: 6.8-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: CCD / Date: Jun 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→35.17 Å / Num. obs: 34344 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.0487 / Net I/σ(I): 8.86 |
Reflection shell | Highest resolution: 1.47 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1C6T Resolution: 1.473→35.169 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.473→35.169 Å
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Refine LS restraints |
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LS refinement shell |
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