+Open data
-Basic information
Entry | Database: PDB / ID: 4hqf | ||||||
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Title | Crystal structure of Plasmodium falciparum TRAP, I4 form | ||||||
Components | Thrombospondin-related anonymous protein, TRAP | ||||||
Keywords | CELL ADHESION / malaria / parasite motility / I domain / TSR domain / receptor on sporozoite / vaccine target / sporozoite surface | ||||||
Function / homology | Function and homology information microneme / symbiont entry into host / host cell surface receptor binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 4hqf.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hqf.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/4hqf ftp://data.pdbj.org/pub/pdb/validation_reports/hq/4hqf | HTTPS FTP |
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-Related structure data
Related structure data | 4hqkC 4hqlC 4hqnC 4hqoC 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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Unit cell |
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-Components
#1: Protein | Mass: 31766.037 Da / Num. of mol.: 1 / Fragment: adhesive domains (UNP residues 26-299) / Mutation: C55G, N132S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: TRAP, PF13_0201 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q76NM2 |
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#2: Chemical | ChemComp-CL / |
#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: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate, 25% PEG4000, 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: 0.97 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2011 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.27 Å / Num. all: 14536 / Num. obs: 14268 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.89 % / Rsym value: 0.16 / Net I/σ(I): 11.26 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.69 / Rsym value: 1.12 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHU Resolution: 2.2→34.855 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 25.24 / 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: 2.2→34.855 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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