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- PDB-4hql: Crystal structure of magnesium-loaded Plasmodium vivax TRAP protein -

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Basic information

Entry
Database: PDB / ID: 4hql
TitleCrystal structure of magnesium-loaded Plasmodium vivax TRAP protein
ComponentsSporozoite surface protein 2
KeywordsCELL ADHESION / malaria / parasite motility / VWA domain / TSR domain / receptor on sporozoite / vaccine target / sporozoite surface
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Thrombospondin type 1 domain / von Willebrand factor, type A 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 (vWF) type A domain ...TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Thrombospondin type 1 domain / von Willebrand factor, type A 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 (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Single Sheet / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sporozoite surface protein 2
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.241 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sporozoite surface protein 2
B: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7428
Polymers59,9702
Non-polymers7726
Water9,674537
1
A: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3714
Polymers29,9851
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3714
Polymers29,9851
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.601, 97.963, 159.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sporozoite surface protein 2 / Thrombospondin repeat anonymous protein / TRAP


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 beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 15% PEG20000, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.24→41.72 Å / Num. all: 45629 / Num. obs: 45447 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.085 / Net I/σ(I): 13.73
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.36 / Rsym value: 0.353 / % possible all: 99.1

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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: 2.241→41.72 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 2288 5.04 %
Rwork0.1629 --
obs0.165 45378 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.241→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 46 537 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084176
X-RAY DIFFRACTIONf_angle_d1.015631
X-RAY DIFFRACTIONf_dihedral_angle_d12.6581585
X-RAY DIFFRACTIONf_chiral_restr0.071646
X-RAY DIFFRACTIONf_plane_restr0.004721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.241-2.28970.24081500.20232580X-RAY DIFFRACTION97
2.2897-2.3430.19831600.1882624X-RAY DIFFRACTION100
2.343-2.40160.21821390.17842655X-RAY DIFFRACTION100
2.4016-2.46650.25431310.17972671X-RAY DIFFRACTION100
2.4665-2.53910.23621270.18432681X-RAY DIFFRACTION100
2.5391-2.6210.22791530.16872668X-RAY DIFFRACTION100
2.621-2.71470.19841270.16482699X-RAY DIFFRACTION100
2.7147-2.82330.1961330.16062680X-RAY DIFFRACTION100
2.8233-2.95180.20561590.16442670X-RAY DIFFRACTION100
2.9518-3.10740.22261420.16542697X-RAY DIFFRACTION100
3.1074-3.3020.22311440.16412693X-RAY DIFFRACTION100
3.302-3.55680.16961300.15822709X-RAY DIFFRACTION100
3.5568-3.91450.18791400.15092728X-RAY DIFFRACTION100
3.9145-4.48040.17411500.14312723X-RAY DIFFRACTION100
4.4804-5.64260.20011400.14612768X-RAY DIFFRACTION100
5.6426-41.72730.22471630.18362844X-RAY DIFFRACTION98
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)
13.43451.08430.99892.18010.42393.8592-0.03650.37510.3454-0.29550.04260.0026-0.17380.0229-0.01910.17870.04080.02620.18360.04370.205225.5233-15.065-11.4901
23.40612.06271.40489.94889.38188.9647-0.0013-0.03840.24010.89130.21120.31580.14660.0996-0.24171.50210.04220.22570.5467-0.12911.013515.5741-42.7884-56.398
37.85792.8581-6.2990.8451-2.34415.01870.1678-0.7113-0.00840.16050.3187-0.3274-0.0189-0.6041-0.18870.5893-0.0023-0.07020.85230.36640.222211.9479-10.3608-39.7883
44.2587-0.01271.17574.31150.00435.19460.0524-0.0005-0.38610.1943-0.1967-0.77070.60890.91310.15140.34190.0780.00810.46670.17810.421127.2852-5.1853-59.1308
56.61745.8452-2.06376.02-3.41896.2018-0.0188-0.2371-0.3338-0.019-0.1057-0.05570.0958-0.06770.1470.23130.0652-0.02260.24510.08330.280514.10581.8391-63.6678
67.35150.02163.21267.42731.0972.0307-0.64960.18192.33220.64820.41880.8764-2.3371-0.84520.38240.74750.1341-0.09190.73890.11010.586414.355311.7965-57.077
71.93977.12351.82518.573-9.81752.03490.2875-0.30440.69790.70780.40520.0047-0.7216-0.3165-0.40880.9788-0.08580.11040.57980.05330.375814.6457-2.5558-41.0831
88.9118-1.4284-7.52353.05911.37828.4123-0.00010.28970.39250.0045-0.10050.1506-0.0924-0.09380.10780.1265-0.0077-0.0630.1933-0.00220.1834-6.836-16.3016-4.1493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 283 )
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 50 )
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 163 )
5X-RAY DIFFRACTION5chain 'B' and (resid 164 through 199 )
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 215 )
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 239 )
8X-RAY DIFFRACTION8chain 'B' and (resid 240 through 283 )

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