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Yorodumi- PDB-5klh: Crystal Structure of Trypanosoma brucei Procyclic Specific Surfac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5klh | ||||||
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Title | Crystal Structure of Trypanosoma brucei Procyclic Specific Surface Antigen-2 | ||||||
Components | Surface glycoprotein | ||||||
Keywords | MEMBRANE PROTEIN / Bi-lobed architecture / surface protein / putative sensor | ||||||
Function / homology | membrane => GO:0016020 / Surface glycoprotein Function and homology information | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.646 Å | ||||||
Authors | Ramaswamy, R. / Parker, M.L. / Boulanger, M.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Protein Sci. / Year: 2016 Title: Structural characterization reveals a novel bilobed architecture for the ectodomains of insect stage expressed Trypanosoma brucei PSSA-2 and Trypanosoma congolense ISA. Authors: Ramaswamy, R. / Goomeshi Nobary, S. / Eyford, B.A. / Pearson, T.W. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5klh.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5klh.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 5klh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5klh_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 5klh_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 5klh_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 5klh_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/5klh ftp://data.pdbj.org/pub/pdb/validation_reports/kl/5klh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25393.121 Da / Num. of mol.: 2 / Fragment: residues 40-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / References: UniProt: Q26806 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M (NH4)2SO4, 0.1 M Bis-tris pH 6.5, and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.646→56.95 Å / Num. obs: 45400 / % possible obs: 92.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.646→47.122 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.79 Å2 / Biso mean: 21.38 Å2 / Biso min: 6.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.646→47.122 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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