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Open data
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Basic information
Entry | Database: PDB / ID: 7log | ||||||
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Title | T4 lysozyme mutant L99A in complex with 3-butylpyridine | ||||||
![]() | Lysozyme | ||||||
![]() | PROTEIN BINDING / HYDROLASE / mutant / lysozyme / small molecule / L99A / complex | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Energy penalties enhance flexible receptor docking in a model cavity. Authors: Kamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.6 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7loaC ![]() 7lobC ![]() 7locC ![]() 7lodC ![]() 7loeC ![]() 7lofC ![]() 7lojC ![]() 7lx6C ![]() 7lx7C ![]() 7lx8C ![]() 7lx9C ![]() 7lxaC ![]() 4w57S 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
#1: Protein | Mass: 19691.541 Da / Num. of mol.: 1 / Mutation: L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: D9IEF7, lysozyme | ||||||
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#2: Chemical | ChemComp-Y8J / | ||||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: Isopropanol, PEG 4000, Tris-Cl pH 8.0, Beta-mercaptoethanol, 2-hyrdoxyethyl disulfide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2020 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9539 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 0.99→52.18 Å / Num. obs: 108816 / % possible obs: 96.6 % / Redundancy: 16.5 % / Biso Wilson estimate: 11.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.009 / Rrim(I) all: 0.037 / Net I/σ(I): 30.2 / Num. measured all: 1792794 / Scaling rejects: 290 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4W57 Resolution: 0.99→52.176 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.17 / 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: 34.15 Å2 / Biso mean: 13.7836 Å2 / Biso min: 7.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.99→52.176 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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