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- PDB-3vdk: Crystal structure of circumsporozoite protein aTSR domain, R32 pl... -

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Basic information

Entry
Database: PDB / ID: 3vdk
TitleCrystal structure of circumsporozoite protein aTSR domain, R32 platinum-bound 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 / SAD / Resolution: 1.847 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Circumsporozoite (CS) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0972
Polymers8,9021
Non-polymers1951
Water93752
1


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

A: Circumsporozoite (CS) protein
hetero molecules

A: Circumsporozoite (CS) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2916
Polymers26,7063
Non-polymers5853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5010 Å2
ΔGint-78 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.534, 66.534, 86.488
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-515-

HOH

21A-544-

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: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.07195 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07195 Å / Relative weight: 1
ReflectionResolution: 1.847→50 Å / Num. all: 6265 / Num. obs: 6265 / % possible obs: 98.1 % / Observed criterion σ(I): 5 / Redundancy: 6.5 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 42.6
Reflection shellResolution: 1.847→1.92 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6375 / % possible all: 86.9

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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: SAD / Resolution: 1.847→33.267 Å / SU ML: 0.28 / σ(F): 0.16 / Phase error: 22.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 625 9.98 %RANDOM
Rwork0.1759 ---
obs0.18 6264 96.25 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.642 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.1249 Å20 Å20 Å2
2---11.1249 Å20 Å2
3---7.745 Å2
Refinement stepCycle: LAST / Resolution: 1.847→33.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 1 52 620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006581
X-RAY DIFFRACTIONf_angle_d1.042779
X-RAY DIFFRACTIONf_dihedral_angle_d13.907228
X-RAY DIFFRACTIONf_chiral_restr0.0682
X-RAY DIFFRACTIONf_plane_restr0.004101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.847-2.03260.24991370.19621255X-RAY DIFFRACTION88
2.0326-2.32670.24111550.16311428X-RAY DIFFRACTION99
2.3267-2.93110.24661630.17261452X-RAY DIFFRACTION99
2.9311-33.27240.19341700.17771504X-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)
10.10430.0822-0.0460.0655-0.04090.0255-0.12610.5208-0.5636-0.41770.0011-0.47430.17870.24620.00010.3495-0.0142-0.01060.36130.01080.3227-4.863125.578421.4149
20.3505-0.0325-0.23560.38740.00650.1587-0.02940.2373-0.066-0.4450.0237-0.0188-0.0161-0.08010.00020.2867-0.00030.01130.28590.010.20047.147535.585325.7625
30.0516-0.05410.04210.0548-0.04240.0329-0.025-0.42550.16070.2172-0.0993-0.0842-0.1848-0.27540.00020.22180.0233-0.01220.2615-0.03130.263816.108637.198132.138
40.49750.54490.39660.73180.18130.6410.1262-0.0028-0.29540.0906-0.0842-0.22510.2019-0.0768-00.22240.0096-0.01230.24690.02070.26359.758728.154433.3941
50.840.42790.78650.36650.31240.7944-0.35420.5004-0.368-0.25330.2891-0.21080.19280.2876-0.03590.34890.04750.07150.2411-0.04680.514224.631828.684424.3089
60.04260.3196-0.24453.0841-2.30221.7289-0.66310.22361.2396-1.15460.30340.29920.228-0.2627-0.03010.3687-0.05470.02760.3532-0.09570.514920.896935.749520.5271
70.0434-0.07670.00450.4656-0.21770.11540.2142-0.1040.09380.09810.1972-0.1888-0.06240.29320.00030.3048-0.00820.04740.3405-0.060.399911.017725.913225.6023
80.0837-0.0655-0.07730.20970.15930.12340.3024-0.6470.33750.30560.01340.2089-0.0255-0.37080.0010.3444-0.01210.09030.47760.03870.3994-6.321628.283540.8415
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 347:354)
6X-RAY DIFFRACTION6chain 'A' and (resseq 355:359)
7X-RAY DIFFRACTION7chain 'A' and (resseq 360:370)
8X-RAY DIFFRACTION8chain 'A' and (resseq 371:376)

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