+Open data
-Basic information
Entry | Database: PDB / ID: 1zur | ||||||
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Title | Crystal structure of spin labeled T4 Lysozyme (V131R1F) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / NITROXIDE SPIN LABEL / EPR / MODIFIED CYSTEINE | ||||||
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 / Resolution: 1.6 Å | ||||||
Authors | Fleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of spin labeled T4 Lysozyme (V131R1F) Authors: Fleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L. #1: Journal: Biochemistry / Year: 2000 Title: Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure Authors: Langen, R. / Oh, K.J. / Cascio, D. / 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 | 1zur.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zur.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zur ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zur | 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
#1: Protein | Mass: 18632.375 Da / Num. of mol.: 1 / Mutation: C54T, C97A, V131C 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme | ||
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#2: Chemical | ChemComp-R1F / | ||
#3: Chemical | ChemComp-CL / #4: 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: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol, isopropanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. all: 27100 / Num. obs: 25979 / % possible obs: 96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.134 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 4.6 / Num. unique all: 2571 / Rsym value: 0.458 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C6T Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.372 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.981 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→51.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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