+Open data
-Basic information
Entry | Database: PDB / ID: 7l3f | ||||||
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Title | T4 Lysozyme L99A - 4-iodotoluene - RT | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / RT / 4-iodotoluene / L99A | ||||||
Function / homology | Function and homology information 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 | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Fischer, M. / Bradford, S.Y.C. | ||||||
Citation | Journal: Chem Sci / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l3f.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l3f.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 7l3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/7l3f ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l3f | HTTPS FTP |
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-Related structure data
Related structure data | 7l37C 7l38C 7l39C 7l3aC 7l3bC 7l3cC 7l3dC 7l3eC 7l3gC 7l3hC 7l3iC 7l3jC 7l3kC 4w51S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-XQM / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.61 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||
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: 1.49→35.94 Å / Num. obs: 35258 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.7 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4w51 Resolution: 1.49→35.934 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.96 / 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: 98.52 Å2 / Biso mean: 23.6638 Å2 / Biso min: 12.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→35.934 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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