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Open data
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Basic information
Entry | Database: PDB / ID: 5ki8 | ||||||
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Title | PSEUDO T4 LYSOZYME MUTANT - Y88PHE-BR | ||||||
![]() | Endolysin | ||||||
![]() | HYDROLASE / HALOGEN BONDS / 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 | ![]() ![]() ![]() | ||||||
![]() | Scholfield, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Energy Relationships of Halogen Bonds in Proteins. Authors: Scholfield, M.R. / Ford, M.C. / Carlsson, A.C. / Butta, H. / Mehl, R.A. / Ho, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.1 KB | Display | ![]() |
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Full document | ![]() | 417.1 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5khzC ![]() 5ki1C ![]() 5ki2C ![]() 5ki3C ![]() 5kigC ![]() 5kiiC ![]() 5kimC ![]() 5kioC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19520.141 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HED / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.4M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.9 PH range: 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→45.7 Å / Num. obs: 28167 / % possible obs: 95 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.64 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.3 / Num. measured obs: 2068 / % possible all: 71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L63 Resolution: 1.55→45.7 Å / SU ML: 0.169 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→45.7 Å
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Refine LS restraints |
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LS refinement shell |
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