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Open data
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Basic information
Entry | Database: PDB / ID: 7l3d | ||||||
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Title | T4 Lysozyme L99A - 3-iodotoluene - RT | ||||||
![]() | Endolysin | ||||||
![]() | HYDROLASE / RT / 3-iodotoluene / L99A | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Fischer, M. / Bradford, S.Y.C. | ||||||
![]() | ![]() Title: Temperature artifacts in protein structures bias ligand-binding predictions. Authors: Bradford, S.Y.C. / El Khoury, L. / Ge, Y. / Osato, M. / Mobley, D.L. / Fischer, 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 | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7l37C ![]() 7l38C ![]() 7l39C ![]() 7l3aC ![]() 7l3bC ![]() 7l3cC ![]() 7l3eC ![]() 7l3fC ![]() 7l3gC ![]() 7l3hC ![]() 7l3iC ![]() 7l3jC ![]() 7l3kC ![]() 4w51S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18620.387 Da / Num. of mol.: 1 / Mutation: R12G/I137R/L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 103 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/XQJ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/XQJ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TRS / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-XQJ / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris- ...Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris-hydrochloride (pH 8), 20%-26% (w/v) PEG 4000, 70-170 mM lithium citrate, 8%-18% 2-propanol, 50 mM 2-mercaptoethanol, and 50 mM 2-hydroxyethyl disulfide Temp details: 291-293 |
-Data collection
Diffraction | Mean temperature: 278 K / Ambient temp details: RT / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.35→52.94 Å / Num. obs: 46564 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.1 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4w51 Resolution: 1.35→46.552 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.73 Å2 / Biso mean: 21.7656 Å2 / Biso min: 11.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→46.552 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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