+Open data
-Basic information
Entry | Database: PDB / ID: 2o7a | ||||||
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Title | T4 lysozyme C-terminal fragment | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Protein folding / protein stability / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å | ||||||
Authors | Echols, N. / Kwon, E. / Marqusee, S.M. / Alber, T. | ||||||
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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Remark 999 | SEQUENCE Residues 171-182 correspond to residues 1-12 in the wild-type structure. The initial 12 ...SEQUENCE Residues 171-182 correspond to residues 1-12 in the wild-type structure. The initial 12 residues have been moved to the C-terminus, with a 6-residue linker (SGGGGA) in between. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o7a.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o7a.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 2o7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/2o7a ftp://data.pdbj.org/pub/pdb/validation_reports/o7/2o7a | HTTPS FTP |
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-Related structure data
Related structure data | 2o4wC 2o79C 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
#1: Protein | Mass: 14038.006 Da / Num. of mol.: 1 / Mutation: 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-ACT / |
#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: 1.84 Å3/Da / Density % sol: 33.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM NaCacodylate pH 5.0, 200 mM NaAcetate, 26% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.82653 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82653 Å / Relative weight: 1 |
Reflection | Resolution: 0.84→20 Å / Num. all: 92458 / Num. obs: 92458 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 4.64 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 0.84→0.87 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9108 / Rsym value: 0.224 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1sx7 Resolution: 0.84→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 0.84→20 Å
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Refine LS restraints |
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