+Open data
-Basic information
Entry | Database: PDB / ID: 3l2x | ||||||
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Title | Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / NITROXIDE SPIN LABEL / EPR / MODIFIED CYSTEINE / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fleissner, M.R. / Cascio, D. / Hubbell, W.L. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX Authors: Fleissner, M.R. / Cascio, D. / Kalai, T. / Hideg, K. / Hubbell, W.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l2x.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l2x.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 3l2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/3l2x ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l2x | HTTPS FTP |
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-Related structure data
Related structure data | 1c6tS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18576.350 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T115C, R119C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E, Lysozyme / Plasmid: pHSe5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme |
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-Non-polymers , 6 types, 164 molecules
#2: Chemical | ChemComp-RXR / [ | ||||||
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#3: Chemical | ChemComp-AZI / | ||||||
#4: Chemical | #5: Chemical | ChemComp-HED / | #6: Chemical | ChemComp-BME / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | EXTENSIVE EPR EXPERIMENTS OF THE DISULFIDE LINKED RXR LIGAND ATTACHED TO T4 LYSOZYME AT DIFFERENT ...EXTENSIVE EPR EXPERIMENT |
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-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: 54.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 2.0M dibasic potassium phosphate and monobasic sodium phosphate, 0.25M sodium chloride, 0.04% sodium azide, saturated with bis(2-hydroxyethyl) disulfide, pH 6.4, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MIRRORS (BLUE OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→80 Å / Num. obs: 18829 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rsym value: 0.072 / Χ2: 1.023 / Net I/σ(I): 12.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1C6T Resolution: 1.8→35.419 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Stereochemistry target values: ML Details: THE RXR LIGAND IS DISUFLDE BONDED TO CYS 115 AND CYS 119, AND WAS MODELED IN AT AN OCCUPANCY OF 0.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.001 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.33 Å2 / Biso mean: 21.209 Å2 / Biso min: 8.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.419 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 25.2491 Å / Origin y: -11.2388 Å / Origin z: 9.4138 Å
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Refinement TLS group |
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