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Yorodumi- PDB-4epi: The crystal structure of pesticin-T4 lysozyme hybrid stabilized b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4epi | ||||||
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Title | The crystal structure of pesticin-T4 lysozyme hybrid stabilized by engineered disulfide bonds | ||||||
Components | Pesticin, Lysozyme Chimera | ||||||
Keywords | TOXIN / HYDROLASE / bacterial toxin | ||||||
Function / homology | Function and homology information metabolic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Seddiki, N. / Fairman, J.W. / Noinaj, N. / Lukacik, P. / Barnard, T. / Buchanan, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural engineering of a phage lysin that targets Gram-negative pathogens. Authors: Lukacik, P. / Barnard, T.J. / Keller, P.W. / Chaturvedi, K.S. / Seddiki, N. / Fairman, J.W. / Noinaj, N. / Kirby, T.L. / Henderson, J.P. / Steven, A.C. / Hinnebusch, B.J. / Buchanan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4epi.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4epi.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 4epi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/4epi ftp://data.pdbj.org/pub/pdb/validation_reports/ep/4epi | HTTPS FTP |
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-Related structure data
Related structure data | 4epaC 4epfSC 4exmC 2lzmS 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: 37338.410 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: I168C,I174C,C219T,L329C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria), (gene. exp.) Enterobacteria phage T4 (virus) Gene: pst, YP_pPCP06, YPPCP1.05c, E / Production host: Escherichia coli (E. coli) / References: UniProt: Q57159, UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Sequence details | PROTEIN IS A CHIMERA COMPRISING RESIDUES 1-167 OF PESTICIN (UNP Q57159) AND RESIDUES 4-165 OF T4 ...PROTEIN IS A CHIMERA COMPRISING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% w/v PEG3350, 0.25 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→45.096 Å / Num. obs: 40579 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.3 % / Rsym value: 0.085 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.74→1.78 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.577 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4EPF AND 2LZM Resolution: 1.74→45.096 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.274 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→45.096 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.784 Å / Total num. of bins used: 20
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