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- PDB-4hqk: Crystal structure of Plasmodium falciparum TRAP, P4212 form -

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Basic information

Entry
Database: PDB / ID: 4hqk
TitleCrystal structure of Plasmodium falciparum TRAP, P4212 form
ComponentsThrombospondin-related anonymous protein, TRAP
KeywordsCELL ADHESION / malaria / parasite motility / VWA 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 / 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 ...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 / 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: 2.249 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 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: Thrombospondin-related anonymous protein, TRAP
B: Thrombospondin-related anonymous protein, TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5093
Polymers46,4132
Non-polymers961
Water2,936163
1
A: Thrombospondin-related anonymous protein, TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3032
Polymers23,2071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thrombospondin-related anonymous protein, TRAP


Theoretical massNumber of molelcules
Total (without water)23,2071
Polymers23,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.707, 117.707, 65.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-404-

HOH

31B-303-

HOH

41B-312-

HOH

51B-322-

HOH

61B-365-

HOH

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Components

#1: Protein Thrombospondin-related anonymous protein, TRAP


Mass: 23206.557 Da / Num. of mol.: 2 / Fragment: closed VWA domain (UNP residues 41-240) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2% PEG400, 2 M ammonium sulfate, EVAPORATION, temperature 298K

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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: Jun 18, 2012
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: 2.249→41.03 Å / Num. all: 22426 / Num. obs: 22401 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rsym value: 0.157 / Net I/σ(I): 10.22
Reflection shellResolution: 2.249→2.29 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.28 / Rsym value: 1 / % possible all: 99.6

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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: 2.249→41.029 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 2240 10 %
Rwork0.1869 --
obs0.1922 22394 99.76 %
all-22426 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.249→41.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 5 163 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033173
X-RAY DIFFRACTIONf_angle_d0.6964285
X-RAY DIFFRACTIONf_dihedral_angle_d10.9181183
X-RAY DIFFRACTIONf_chiral_restr0.05497
X-RAY DIFFRACTIONf_plane_restr0.003555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.29760.35941340.30641201X-RAY DIFFRACTION97
2.2976-2.3510.34961270.27031257X-RAY DIFFRACTION100
2.351-2.40980.31421440.2541226X-RAY DIFFRACTION100
2.4098-2.47490.31681510.25741202X-RAY DIFFRACTION100
2.4749-2.54780.34071260.24341261X-RAY DIFFRACTION100
2.5478-2.630.3071400.22331256X-RAY DIFFRACTION100
2.63-2.7240.30211360.22361229X-RAY DIFFRACTION100
2.724-2.8330.261400.19311254X-RAY DIFFRACTION100
2.833-2.96190.24391380.20211241X-RAY DIFFRACTION100
2.9619-3.1180.24881410.19721259X-RAY DIFFRACTION100
3.118-3.31330.2831380.1871255X-RAY DIFFRACTION100
3.3133-3.5690.23071420.16921266X-RAY DIFFRACTION100
3.569-3.92790.20711420.14831272X-RAY DIFFRACTION100
3.9279-4.49560.1741410.13351284X-RAY DIFFRACTION100
4.4956-5.66170.19971460.15061297X-RAY DIFFRACTION100
5.6617-41.03620.221540.20751394X-RAY DIFFRACTION100
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)
13.81170.7734-3.63375.556-4.8939.19410.15631.0390.3172-1.61330.2516-0.1991-0.1062-1.7464-0.60320.77070.06620.06270.42210.03640.306187.621347.55658.7886
22.6430.05770.11834.5725-0.5254.23830.21940.1875-0.1201-0.4407-0.04930.01870.2164-0.168-0.16990.28730.0512-0.00090.2679-0.00360.313684.293939.252816.1719
37.2951-1.47261.59915.57170.29479.41960.2230.3080.0746-0.5974-0.0159-0.7614-0.08912.035-0.31490.4781-0.03120.15220.4345-0.01160.5493100.176947.198114.968
44.4336-1.9376-0.60351.69211.37088.20990.1957-0.2990.77850.1225-0.1073-0.4481-0.84730.6019-0.1540.5989-0.04840.10120.2363-0.04380.543991.559753.936120.9958
56.74253.74860.22485.0171.24064.62960.3519-0.0880.5644-0.417-0.24480.1532-1.3006-0.3814-0.09040.76010.10520.08470.31490.01480.446781.78660.545521.8584
69.79483.9443-2.19632.5835-2.03497.38160.44021.27470.7701-0.780.26380.1699-0.6381-0.8784-0.47950.73020.25540.09780.52430.08490.499978.175553.266111.1219
78.3472-2.3781.3188.19563.8146.95970.13861.2669-0.827-1.0658-0.06840.2599-0.01530.44150.04340.5199-0.096-0.01940.337-0.05230.446383.498811.41411.1081
84.59923.7721-6.86473.0558-5.59382.03950.4983-0.65780.31240.5471-0.5919-0.2037-0.20380.55460.1530.3516-0.05720.0030.492-0.04080.385697.586721.08226.0795
98.44670.59780.39257.31474.17458.1840.04240.9009-0.1318-0.8774-0.04090.0037-0.0617-0.02440.0960.36770.01830.00130.17130.05330.282686.234816.465910.9561
104.39610.61212.37372.90670.3448.6031-0.1529-0.04340.362-0.32660.0669-0.0355-0.3112-0.3170.08790.30840.07190.0480.2380.00270.33684.439523.415618.0464
117.6918-3.0240.38717.4933-2.24827.154-0.1073-0.0134-0.20410.01990.08150.61440.1575-0.7169-0.00980.3331-0.04720.05760.18830.01230.348977.049611.07420.8048
127.58613.5726-0.77225.90790.18917.6242-0.3549-0.5065-0.97370.36270.02740.33570.9123-0.42470.2880.49120.08620.05250.22580.05580.434580.09614.396625.1539
135.3973-2.1420.92829.27233.27535.2459-0.429-0.3074-0.14070.16730.44080.3921-0.5630.5065-0.00230.6236-0.04080.09110.43060.00410.297791.60672.792927.6257
148.28944.3827-2.82193.9993-4.81017.5274-0.8996-0.2537-0.7895-0.501-0.026-0.4181.45870.56220.73880.68850.13560.12520.38010.0160.580692.4731-1.971821.6191
158.9136-0.52272.00666.02381.26348.46550.68670.1451-0.8248-0.5472-0.6512-0.46770.52250.44850.08750.51250.04820.10.3286-0.0070.452393.99617.109812.7364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 240 )
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 54 )
8X-RAY DIFFRACTION8chain 'B' and (resid 55 through 67 )
9X-RAY DIFFRACTION9chain 'B' and (resid 68 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 132 )
11X-RAY DIFFRACTION11chain 'B' and (resid 133 through 167 )
12X-RAY DIFFRACTION12chain 'B' and (resid 168 through 190 )
13X-RAY DIFFRACTION13chain 'B' and (resid 191 through 203 )
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 219 )
15X-RAY DIFFRACTION15chain 'B' and (resid 220 through 239 )

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