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- PDB-3vdj: Crystal structure of circumsporozoite protein aTSR domain, R32 na... -

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Basic information

Entry
Database: PDB / ID: 3vdj
TitleCrystal structure of circumsporozoite protein aTSR domain, R32 native form
ComponentsCircumsporozoite (CS) protein
KeywordsCELL INVASION / TSR / aTSR
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / : / Plasmodium circumsporozoite protein / 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 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsDoud, M.B. / Koksal, A.C. / Mi, L.Z. / Song, G. / Lu, C. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unexpected fold in the circumsporozoite protein target of malaria vaccines.
Authors: Doud, M.B. / Koksal, A.C. / Mi, L.Z. / Song, G. / Lu, C. / Springer, T.A.
History
DepositionJan 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)8,9021
Polymers8,9021
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Circumsporozoite (CS) protein

A: Circumsporozoite (CS) protein

A: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)26,7063
Polymers26,7063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4760 Å2
ΔGint-29 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.515, 66.515, 85.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-464-

HOH

31A-469-

HOH

41A-470-

HOH

51A-489-

HOH

61A-499-

HOH

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Components

#1: Protein Circumsporozoite (CS) protein


Mass: 8902.075 Da / Num. of mol.: 1 / Fragment: alpha-TSR domain (UNP residues 310-374)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFC0210c / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q7K740
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M citrate, pH 4.0, 1 M lithium chloride, 20% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. all: 8234 / Num. obs: 8160 / % possible obs: 99.1 % / Observed criterion σ(I): 5 / Redundancy: 4.9 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.7
Reflection shellResolution: 1.698→1.73 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VDK

3vdk


Resolution: 1.698→47.774 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 379 4.65 %RANDOM
Rwork0.1701 ---
obs0.1716 8157 98.99 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.857 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5904 Å20 Å20 Å2
2---3.5904 Å20 Å2
3---9.2174 Å2
Refinement stepCycle: LAST / Resolution: 1.698→47.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 103 670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006581
X-RAY DIFFRACTIONf_angle_d0.972779
X-RAY DIFFRACTIONf_dihedral_angle_d13.325228
X-RAY DIFFRACTIONf_chiral_restr0.06682
X-RAY DIFFRACTIONf_plane_restr0.004101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.698-1.94390.27161160.23182516X-RAY DIFFRACTION98
1.9439-2.44910.19751160.14942606X-RAY DIFFRACTION100
2.4491-47.79290.18841470.16642656X-RAY DIFFRACTION99
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)
16.97575.88744.66955.21634.13523.2782-0.1231.0242-0.4688-0.43210.213-0.0290.15550.0701-0.13120.2006-0.0047-0.03370.22520.00280.1834-5.0051-12.97286.8709
27.36022.5630.69547.87722.64456.5949-0.14350.2398-0.1925-0.4820.05740.0171-0.1514-0.07760.10190.10760.02170.03060.11190.00660.09127.163-2.870211.1817
39.2056-4.53942.78773.3528-4.44079.2773-0.156-0.2056-0.27280.41050.0559-0.2528-0.16220.22970.08650.12210.0087-0.02680.1636-0.04360.148616.1264-1.295517.5941
42.041.2133-1.76692.0116-0.09212.83580.01-0.3545-0.38320.1260.07-0.36290.21880.2323-0.05350.11120.0164-0.02040.1317-0.00680.17129.7155-10.331518.8574
57.5597-0.71132.01171.9866-4.09918.5144-0.30.1846-0.4273-0.13870.1063-0.48610.19560.05920.15480.1474-0.00170.02990.1343-0.0740.236922.9605-6.69058.043
68.7642.5641-7.71723.0384-3.29838.6038-0.2732-0.1754-0.6277-0.22770.062-0.20270.5510.48590.21870.16910.030.00350.2065-0.08160.20710.9573-12.619411.0456
75.5419-4.7375-5.56424.04874.83848.6861-0.3269-0.1843-0.24040.5657-0.17470.16280.3405-0.11690.29230.1867-0.03060.03050.23730.03230.1798-6.3895-9.882226.1113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 306:312)
2X-RAY DIFFRACTION2chain 'A' and (resseq 313:322)
3X-RAY DIFFRACTION3chain 'A' and (resseq 323:327)
4X-RAY DIFFRACTION4chain 'A' and (resseq 328:346)
5X-RAY DIFFRACTION5chain 'A' and (resseq 347:359)
6X-RAY DIFFRACTION6chain 'A' and (resseq 360:370)
7X-RAY DIFFRACTION7chain 'A' and (resseq 371:376)

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