+Open data
-Basic information
Entry | Database: PDB / ID: 2o79 | ||||||
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Title | T4 lysozyme with C-terminal extension | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / PROTEIN STABILITY / PROTEIN FOLDING / LYSOZYME / CIRCULAR PERMUTANT | ||||||
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 | Llinas, M. / Crowder, S.M. / Echols, N. / Alber, T. / Marqusee, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment. Authors: Cellitti, J. / Llinas, M. / Echols, N. / Shank, E.A. / Gillespie, B. / Kwon, E. / Crowder, S.M. / Dahlquist, F.W. / Alber, T. / Marqusee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o79.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o79.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 2o79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o79_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 2o79_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 2o79_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2o79_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/2o79 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/2o79 | HTTPS FTP |
-Related structure data
Related structure data | 2o4wC 2o7aC 1sx7S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19015.711 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 / Plasmid: pET27K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLacI / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 2.66 Å3/Da / Density % sol: 53.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.9 M K2HPO4, 1.1 M NaH2PO4, pH 6.6, 0.25 M NaCl, 49.0 mM oxidized B mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 19210 / Num. obs: 19210 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 14.76 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 52.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 14.5 / Num. unique all: 1760 / Rsym value: 0.214 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1sx7 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.668 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.099 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.308 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.897 Å / Total num. of bins used: 10
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