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- PDB-4hqf: Crystal structure of Plasmodium falciparum TRAP, I4 form -

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Basic information

Entry
Database: PDB / ID: 4hqf
TitleCrystal structure of Plasmodium falciparum TRAP, I4 form
ComponentsThrombospondin-related anonymous protein, TRAP
KeywordsCELL 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
Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor, type A domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A ...Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor, type A domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thrombospondin-related anonymous protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSong, G. / Koksal, A.C. / Lu, C. / Springer, T.A.
CitationJournal: 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
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombospondin-related anonymous protein, TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8012
Polymers31,7661
Non-polymers351
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.220, 110.220, 47.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Thrombospondin-related anonymous protein, TRAP


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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.2→2.26 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.69 / Rsym value: 1.12 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHU

1shu


Resolution: 2.2→34.855 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 715 5.01 %
Rwork0.1729 --
obs0.1752 14268 98.18 %
all-14536 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 1 144 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081598
X-RAY DIFFRACTIONf_angle_d1.0972159
X-RAY DIFFRACTIONf_dihedral_angle_d12.532598
X-RAY DIFFRACTIONf_chiral_restr0.074250
X-RAY DIFFRACTIONf_plane_restr0.005281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.36771420.28452671X-RAY DIFFRACTION98
2.37-2.60850.30061430.22992748X-RAY DIFFRACTION100
2.6085-2.98570.241420.19592710X-RAY DIFFRACTION99
2.9857-3.7610.22321430.15752699X-RAY DIFFRACTION98
3.761-34.8590.16011450.14052724X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.46961.5076-0.97715.310.47846.28790.11160.0921-0.1059-0.20460.02020.1496-0.1908-0.047-0.13410.253-0.006-0.04290.15490.01850.185519.312521.37251.7357
26.5228-0.1499-1.1144.3892-0.85835.14730.020.1994-0.1373-0.24580.1018-0.1085-0.0152-0.0017-0.04450.2024-0.055-0.06390.21810.01270.214721.306614.1069-2.412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 41:103)
2X-RAY DIFFRACTION2chain 'A' and (resseq 104:215)

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