+Open data
-Basic information
Entry | Database: PDB / ID: 2q9d | ||||||
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Title | Structure of spin-labeled T4 lysozyme mutant A41R1 | ||||||
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 / EPR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Guo, Z. / Cascio, D. / Hideg, K. / Hubbell, W.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme. Authors: Guo, Z. / Cascio, D. / 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 | 2q9d.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q9d.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/2q9d ftp://data.pdbj.org/pub/pdb/validation_reports/q9/2q9d | HTTPS FTP |
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-Related structure data
Related structure data | 2q9eC 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: 18660.428 Da / Num. of mol.: 1 / Mutation: C54T, C97A 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-MTN / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 294 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 294K |
-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: Feb 10, 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: 38697 / Num. obs: 38697 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rsym value: 0.08 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.235 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZM Resolution: 1.4→10 Å / Num. parameters: 14007 / Num. restraintsaints: 16573 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1556 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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