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Open data
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Basic information
Entry | Database: PDB / ID: 7kww | ||||||
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Title | X-ray Crystal Structure of PlyCB Mutant K59H | ||||||
![]() | PlyCB | ||||||
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Function / homology | : / Streptococcus virus C1, PlyCB / killing of cells of another organism / identical protein binding / Endolysin PlyC, small cell-wall binding subunit![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Williams, D.E. / Broendum, S.S. / Hayes, B.K. / Drinkwater, N. / McGowan, S. | ||||||
![]() | ![]() Title: High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus. Authors: Broendum, S.S. / Williams, D.E. / Hayes, B.K. / Kraus, F. / Fodor, J. / Clifton, B.E. / Geert Volbeda, A. / Codee, J.D.C. / Riley, B.T. / Drinkwater, N. / Farrow, K.A. / Tsyganov, K. / ...Authors: Broendum, S.S. / Williams, D.E. / Hayes, B.K. / Kraus, F. / Fodor, J. / Clifton, B.E. / Geert Volbeda, A. / Codee, J.D.C. / Riley, B.T. / Drinkwater, N. / Farrow, K.A. / Tsyganov, K. / Heselpoth, R.D. / Nelson, D.C. / Jackson, C.J. / Buckle, A.M. / McGowan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.4 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kwtC ![]() 7kwyC ![]() 4f87S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8008.106 Da / Num. of mol.: 2 / Mutation: K59H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M HEPES (pH 6.0), 0.2M sodium citrate, 25% methylpentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→36.78 Å / Num. obs: 16685 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 32.42 Å2 / CC1/2: 0.992 / CC star: 0.998 / Net I/σ(I): 22.52 |
Reflection shell | Resolution: 1.8→1.865 Å / Mean I/σ(I) obs: 2.06 / Num. unique obs: 1637 / CC1/2: 0.818 / CC star: 0.949 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4F87 Resolution: 1.8→36.78 Å / SU ML: 0.1875 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1348 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.78 Å
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Refine LS restraints |
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LS refinement shell |
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