+Open data
-Basic information
Entry | Database: PDB / ID: 8ok4 | ||||||
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Title | Variant Surface Glycoprotein VSG11wt-Oil | ||||||
Components | Variant surface glycoprotein | ||||||
Keywords | MEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation | ||||||
Function / homology | Trypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å | ||||||
Authors | Zeelen, J.P. / Stebbins, C.E. / Aresta-Branco, F. / Foti, K. | ||||||
Funding support | 1items
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Citation | Journal: Plos Negl Trop Dis / Year: 2023 Title: A structural classification of the variant surface glycoproteins of the African trypanosomey. Authors: Dakovic, S. / Zeelen, J.P. / Gkeka, A. / Chandra, M. / van Straaten, M. / Foti, K. / Zhong, J. / Vlachou, E.P. / Aresta-Branco, F. / Verdi, J.P. / Papavasiliou, F.N. / Stebbins, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ok4.cif.gz | 229.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ok4.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ok4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/8ok4 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/8ok4 | HTTPS FTP |
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-Related structure data
Related structure data | 8ok5C 8ok6C 8ok7C 8ok8C 8onhC 8q0eC 8q0pC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45175.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES126.15 / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: B3GVS7 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-GLC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.96 % / Description: hexagonal |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.7 M NaKTartrate, 100 mM Tris/HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→40.94 Å / Num. obs: 99764 / % possible obs: 99.91 % / Redundancy: 9.4 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.79 |
Reflection shell | Resolution: 1.23→1.274 Å / Rmerge(I) obs: 1.777 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 9827 / CC1/2: 0.748 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.23→40.94 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.76 / Stereochemistry target values: ML
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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 max: 83.36 Å2 / Biso mean: 22.2497 Å2 / Biso min: 8.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.23→40.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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