+Open data
-Basic information
Entry | Database: PDB / ID: 5wa2 | ||||||
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Title | Crystal structure of Toxoplasma gondii SAG3 (SRS57) | ||||||
Components | Surface antigen | ||||||
Keywords | MEMBRANE PROTEIN / surface antigen glycoprotein (SAG) / tandem beta-sandwich | ||||||
Function / homology | Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / membrane => GO:0016020 / Surface antigen Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.591 Å | ||||||
Authors | Parker, M.L. / Boulanger, M.J. | ||||||
Citation | Journal: To be published Title: A Toxoplasma lectin-specific activity for sulfated proteoglycans thought to promote infection competency is not dependent on TgSRS57 (TgSAG3) Authors: Pszenny, V. / Parker, M.L. / Ramaswamy, R. / Grigg, M.E. / 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 | 5wa2.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wa2.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wa2_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 5wa2_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 5wa2_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 5wa2_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5wa2 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5wa2 | HTTPS FTP |
-Related structure data
Related structure data | 1kzqS 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
#1: Protein | Mass: 33802.996 Da / Num. of mol.: 1 / Fragment: UNP residues 38-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: SAG3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BJ39 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→37.472 Å / Num. obs: 40027 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1927 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KZQ Resolution: 1.591→37.472 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.27 Å2 / Biso mean: 22.9616 Å2 / Biso min: 10.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.591→37.472 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: 14 / % reflection obs: 100 %
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