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Open data
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Basic information
Entry | Database: PDB / ID: 6z8h | ||||||
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Title | Crystal structure of Variant Surface Glycoprotein VSG13 | ||||||
![]() | Variant surface glycoprotein MITat 1.13 | ||||||
![]() | MEMBRANE PROTEIN / Variant Surface Glycoprotein / Immune Recognition / Immune Evasion / Trypanosomiasis | ||||||
Function / homology | Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response / plasma membrane / Variant surface glycoprotein MITat 1.13![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stebbins, C.E. / Hempelmann, A. / Van Straaten, M. / Zeelen, J. | ||||||
![]() | ![]() Title: Structure of trypanosome coat protein VSGsur and function in suramin resistance. Authors: Zeelen, J. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Halg, S. / Wiedemar, N. / Maser, P. / Papavasiliou, F.N. / Stebbins, C.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 441.9 KB | Display | ![]() |
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PDB format | ![]() | 335.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 44.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z79C ![]() 6z7bC ![]() 6z7cC ![]() 6z7dC ![]() 6z7eC ![]() 6z8gSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53771.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Glycosylated at N260 / Source: (natural) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8-2.0 M (NH4)2SO4, 100 mM Tris.Cl pH 8.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.378→48.14 Å / Num. obs: 155980 / % possible obs: 97.09 % / Redundancy: 3 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.03368 / Net I/σ(I): 8.07 |
Reflection shell | Resolution: 1.378→1.428 Å / Num. unique obs: 15141 / CC1/2: 0.84 / % possible all: 94.49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Z8G Resolution: 1.38→48.14 Å / SU ML: 0.1897 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.7523 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: 31.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→48.14 Å
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Refine LS restraints |
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LS refinement shell |
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