+Open data
-Basic information
Entry | Database: PDB / ID: 1xep | ||||||
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Title | Catechol in complex with T4 lysozyme L99A/M102Q | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Graves, A.P. / Brenk, R. / Shoichet, B.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Decoys for docking. Authors: Graves, A.P. / Brenk, R. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xep.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xep.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/1xep ftp://data.pdbj.org/pub/pdb/validation_reports/xe/1xep | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 18617.320 Da / Num. of mol.: 1 / Mutation: L99A, M102Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CAQ / |
#4: Chemical | ChemComp-BME / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: phosphate, pH 6.8-7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 174 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 29343 / % possible obs: 97.7 % / Biso Wilson estimate: 24.7 Å2 |
Reflection shell | Resolution: 1.55→1.61 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 459154.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.7484 Å2 / ksol: 0.332607 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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