+Open data
-Basic information
Entry | Database: PDB / ID: 2ntg | ||||||
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Title | Structure of Spin-labeled T4 Lysozyme Mutant T115R7 | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Nitroxide / Spin label / T4 lysozyme / Electron paramagnetic resonance / EPR | ||||||
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: 1.4 Å | ||||||
Authors | Guo, Z. / Cascio, D. / Hideg, K. / Hubbell, W.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme. Authors: Guo, Z. / Cascio, D. / Hideg, K. / Kalai, T. / 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 | 2ntg.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ntg.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ntg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ntg_validation.pdf.gz | 832.6 KB | Display | wwPDB validaton report |
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Full document | 2ntg_full_validation.pdf.gz | 833.7 KB | Display | |
Data in XML | 2ntg_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2ntg_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2ntg ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2ntg | HTTPS FTP |
-Related structure data
Related structure data | 2igcC 2nthC 2ou8C 2ou9C 3lzmS C: citing same article (ref.) 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: 18630.402 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T115C 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-R7A / |
#3: Chemical | ChemComp-BME / |
#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: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 2.0 M Na/K Phosphate, 240 mM NaCl, 40 mM 2-hydroxyethyl disulfide, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2002 / Details: Parabolic collimating mirrors |
Radiation | Monochromator: Sagitally Focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. all: 38846 / Num. obs: 38846 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.059 / Χ2: 1.069 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 6378 / Rsym value: 0.335 / Χ2: 1.154 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZM Resolution: 1.4→10 Å / Num. parameters: 14223 / Num. restraintsaints: 16726 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.043 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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