+Open data
-Basic information
Entry | Database: PDB / ID: 4hqo | |||||||||
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Title | Crystal structure of Plasmodium vivax TRAP protein | |||||||||
Components | Sporozoite surface protein 2 | |||||||||
Keywords | CELL ADHESION / malaria / gliding motility / VWA domain / TSR domain / extensible beta-ribbon / receptor on sporozoite / vaccine target / sporozoite surface | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | |||||||||
Authors | Song, G. / Koksal, A.C. / Lu, C. / Springer, T.A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Shape change in the receptor for gliding motility in Plasmodium sporozoites. Authors: Song, G. / Koksal, A.C. / Lu, C. / Springer, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hqo.cif.gz | 238.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hqo.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/4hqo ftp://data.pdbj.org/pub/pdb/validation_reports/hq/4hqo | HTTPS FTP |
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-Related structure data
Related structure data | 4hqfC 4hqkC 4hqlC 4hqnC 1shuS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 29985.148 Da / Num. of mol.: 2 / Fragment: adhesive domains (UNP residues 25-283) / Mutation: S42Q, N91S, N128S, S180R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: sal I / Gene: SSP2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9TVF0 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 651 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-NA / | #6: 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: 3.74 Å3/Da / Density % sol: 67.1 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 15% PEG20000, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2011 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.194→42.434 Å / Num. obs: 46935 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rsym value: 0.07 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.194→2.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.69 / Rsym value: 0.315 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHU Resolution: 2.194→42.434 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 20.98 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.194→42.434 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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