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- PDB-4hqn: Crystal structure of manganese-loaded Plasmodium vivax TRAP protein -

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Basic information

Entry
Database: PDB / ID: 4hqn
TitleCrystal structure of manganese-loaded Plasmodium vivax TRAP protein
ComponentsSporozoite surface protein 2
KeywordsCELL ADHESION / malaria / sporozoite motility / VWA domain / TSR domain / extensible beta-ribbon / 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 / 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. ...TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / 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 / 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: 2.196 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: Atomic model / Data collection ...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 / 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 / _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
Revision 2.2Oct 30, 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: Sporozoite surface protein 2
B: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8048
Polymers59,9702
Non-polymers8336
Water9,314517
1
A: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4024
Polymers29,9851
Non-polymers4173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sporozoite surface protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4024
Polymers29,9851
Non-polymers4173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.586, 96.567, 159.521
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 517 / 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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 15% PEG20000, 0.1 M Tris, pH 8.5, 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: 2.196→39.88 Å / Num. obs: 47518 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.13 / Net I/σ(I): 10.61
Reflection shellResolution: 2.196→2.24 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.49 / Rsym value: 0.948 / % possible all: 99.4

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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: 2.196→39.88 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 2403 5.07 %
Rwork0.1725 --
obs0.1744 47440 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 46 517 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074172
X-RAY DIFFRACTIONf_angle_d1.0415626
X-RAY DIFFRACTIONf_dihedral_angle_d13.5451584
X-RAY DIFFRACTIONf_chiral_restr0.069646
X-RAY DIFFRACTIONf_plane_restr0.004720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1955-2.24030.30831150.28742359X-RAY DIFFRACTION89
2.2403-2.2890.31211410.28082628X-RAY DIFFRACTION100
2.289-2.34230.31631330.26042611X-RAY DIFFRACTION100
2.3423-2.40080.29141520.24572648X-RAY DIFFRACTION100
2.4008-2.46580.28691500.23512625X-RAY DIFFRACTION100
2.4658-2.53830.24141460.22282625X-RAY DIFFRACTION100
2.5383-2.62020.21151430.20432638X-RAY DIFFRACTION100
2.6202-2.71380.26651490.20032653X-RAY DIFFRACTION100
2.7138-2.82250.23711320.18682653X-RAY DIFFRACTION100
2.8225-2.95090.24631630.18332648X-RAY DIFFRACTION100
2.9509-3.10640.21191320.182663X-RAY DIFFRACTION100
3.1064-3.30090.23121360.17172669X-RAY DIFFRACTION100
3.3009-3.55570.18471460.15392675X-RAY DIFFRACTION100
3.5557-3.91320.17561550.14692673X-RAY DIFFRACTION100
3.9132-4.47880.16591360.12632699X-RAY DIFFRACTION100
4.4788-5.64030.17351290.13272742X-RAY DIFFRACTION99
5.6403-39.88680.19971450.17062828X-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)
13.06290.98051.59282.74031.0784.35090.07990.16070.0406-0.1504-0.01380.12530.1281-0.2119-0.06940.18760.01830.00680.37080.03160.201122.0475-18.4937-8.3809
29.14124.58127.09665.81813.09888.309-0.16950.9394-0.1895-0.49090.3986-0.043-0.03150.5283-0.19210.1925-0.01210.0810.37440.02980.193728.7839-17.9186-13.149
32.17654.29822.16865.67883.06328.9706-0.29780.8772-0.0334-0.41770.3016-0.57110.12291.5187-0.00460.25480.03310.06740.5763-0.01960.388940.0352-16.1775-13.9278
43.5887-1.9757-5.081610.24329.30692.3022-0.13060.1360.6933-0.60680.0097-0.024-0.42960.2860.04740.26810.00080.01530.40870.12010.347133.1149-6.7739-8.5843
56.29636.6785-4.88377.3711-4.59355.54010.81510.76992.5623-0.74220.434-0.3587-2.1386-0.1858-1.32540.7110.04630.18970.78680.12620.850931.12040.5797-13.4234
63.14682.70111.13139.09972.65851.9336-0.2480.49630.0886-1.06280.37070.053-0.48410.0218-0.10390.40310.0717-0.05870.6010.12540.471418.9641-11.1952-24.6427
75.77237.24911.88362.17538.6239.7495-0.84280.6742-0.7988-0.29942.0796-0.28960.32581.178-1.24611.28610.0377-0.13290.8366-0.20491.238517.7969-44.6921-57.2948
87.60215.39265.37429.95669.23618.5774-0.0987-0.30640.96130.9178-0.51041.13990.4343-0.42550.52051.36360.04480.30750.6142-0.10340.968614.6757-40.9991-55.7886
98.49792.9648-5.48660.1201-1.69623.55970.024-0.7207-0.07760.16960.0343-0.0198-0.0437-0.5403-0.14830.59820.17440.0230.95260.2180.451711.8707-10.2358-39.807
105.63810.84291.15564.9045-0.21745.1631-0.0195-0.0484-0.54150.2207-0.2157-0.86490.5121.01720.21250.390.09530.02730.66060.17650.490927.2955-5.3598-59.1111
112.2995.3171-5.60042.3654-7.07862.2211-0.02370.84970.1411-1.09130.75580.94061.4066-1.6945-0.93720.5469-0.0295-0.05510.72370.09260.49359.8049-4.5254-65.7299
128.86593.03832.60828.9175-0.52774.8981-0.214-0.25620.0350.363-0.2066-0.2289-0.21710.45280.52330.30530.0542-0.0090.45330.07450.262817.1125.8983-62.4581
132.06071.24855.22564.96695.68198.6638-0.7835-0.34721.29250.9730.44040.6321-2.1141-0.55880.50060.76350.0831-0.02810.85650.19260.595614.386511.7849-57.1452
148.15667.5468-7.13846.6255-3.63935.96590.2616-0.12880.11380.6501-0.0921-0.0658-0.8688-0.439-0.08660.66290.0083-0.11351.02080.1690.511514.6363-2.457-41.2156
158.1294-1.8949-7.19792.24231.97268.63120.03350.13180.3767-0.0586-0.05110.1053-0.11410.01190.07030.2109-0.0187-0.0260.45090.0090.2966-6.9616-15.9898-4.1448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 199 )
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 215 )
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 239 )
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 254 )
8X-RAY DIFFRACTION8chain 'A' and (resid 255 through 283 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 163 )
11X-RAY DIFFRACTION11chain 'B' and (resid 164 through 177 )
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 199 )
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 215 )
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 239 )
15X-RAY DIFFRACTION15chain 'B' and (resid 240 through 283 )

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