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- PDB-3vdl: Crystal structure of circumsporozoite protein aTSR domain, P43212 form -

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Basic information

Entry
Database: PDB / ID: 3vdl
TitleCrystal structure of circumsporozoite protein aTSR domain, P43212 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: 2.04 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

Downloads & links

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Assembly

Deposited unit
A: Circumsporozoite (CS) protein
B: Circumsporozoite (CS) protein
C: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)26,7063
Polymers26,7063
Non-polymers00
Water1,62190
1
A: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)8,9021
Polymers8,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)8,9021
Polymers8,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Circumsporozoite (CS) protein


Theoretical massNumber of molelcules
Total (without water)8,9021
Polymers8,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-29 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.372, 63.372, 118.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21B-423-

HOH

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Components

#1: Protein Circumsporozoite (CS) protein


Mass: 8902.075 Da / Num. of mol.: 3 / 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.: 90 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 1.4 M sodium citrate, pH 6.1, 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: 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: 2.04→50 Å / Num. all: 15991 / Num. obs: 15557 / % possible obs: 97.1 % / Observed criterion σ(I): 5 / Redundancy: 11.3 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 21.6
Reflection shellResolution: 2.04→2.11 Å / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.44 / Num. unique all: 15611 / % possible all: 74.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
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: 2.04→43.214 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 781 5.02 %RANDOM
Rwork0.1936 ---
obs0.196 15551 97.21 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8534 Å20 Å20 Å2
2--7.8534 Å20 Å2
3---12.6338 Å2
Refinement stepCycle: LAST / Resolution: 2.04→43.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 90 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071743
X-RAY DIFFRACTIONf_angle_d1.042337
X-RAY DIFFRACTIONf_dihedral_angle_d14.525684
X-RAY DIFFRACTIONf_chiral_restr0.072246
X-RAY DIFFRACTIONf_plane_restr0.005303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.16750.32321060.26762045X-RAY DIFFRACTION83
2.1675-2.33480.26741450.272461X-RAY DIFFRACTION100
2.3348-2.56980.25181350.20812487X-RAY DIFFRACTION100
2.5698-2.94160.21451210.18772523X-RAY DIFFRACTION100
2.9416-3.70580.22561390.17292550X-RAY DIFFRACTION100
3.7058-43.22410.24171350.18432704X-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)
15.7455-0.8873-5.3852.44840.27265.17180.13021.19550.2101-0.24550.22080.3554-0.4669-0.7089-0.32850.26510.02630.03590.3509-0.01420.213417.0321.9099-22.7786
24.26782.10041.79516.9686-2.19593.80210.0151-0.34670.16610.7503-0.07520.4758-0.0197-0.04350.18950.25820.04810.05220.176-0.03050.3691-1.3573.5994-14.6954
35.0859-1.59932.0693.2353-1.01275.1145-0.1404-0.42150.53320.34690.0440.2051-0.5295-0.2580.10250.26550.01420.10840.1573-0.0340.35762.26687.3992-14.8556
45.4843-5.81395.99478.3725-6.45276.5560.92790.2275-0.0856-0.7035-0.55580.43190.6561-0.5067-0.25270.46960.03970.11610.28510.03920.5989-6.8092-1.2259-22.3718
53.0667-2.15542.22676.16320.44612.6832-0.17890.22380.579-0.2999-0.01360.1522-0.40020.01150.20720.249-0.03150.0340.19580.01410.25223.4809-16.1706-15.9819
65.8439-0.44661.6285.40623.94683.53950.3147-0.9434-0.49560.8896-0.18110.98920.0775-0.6936-0.02710.1911-0.03560.15290.32010.11380.4159-5.827-22.9894-10.2251
72.90610.5078-0.02484.89383.83713.70320.3007-0.20880.5660.7672-0.1622-0.17420.1434-0.2619-0.10180.2220.00970.0440.26790.10380.2741-3.9966-12.8058-10.5481
83.45250.0249-4.82876.9699-2.56057.7312-0.08180.0802-0.4665-0.3767-0.20120.4020.272-0.23550.30930.3267-0.0349-0.05620.27630.00540.372-0.6358-29.1708-20.8588
95.3677-2.5784-2.09664.81095.86598.46680.1203-0.02480.1345-0.1886-0.43171.2916-0.0316-0.7750.29270.2789-0.0124-0.03240.29320.07420.4391-6.6378-17.2559-18.3038
102.03850.01781.713.59251.57482.1111-0.0905-0.95270.0231.13430.66930.0485-0.8565-0.018-0.32830.86030.06010.4240.4327-0.05150.8266-4.4860.268-3.746
116.98353.29133.79988.16738.09948.0794-0.13310.52340.2808-1.06680.732-0.4327-0.01280.8359-0.21060.4008-0.03820.02420.31620.09570.18468.2124-20.0078-22.3264
125.44972.3644-2.09255.6896-1.20712.6925-0.0177-0.1371-0.0771-0.0294-0.0919-0.18270.11660.11520.08230.22250.0086-0.01140.1556-0.05210.137221.3215-7.242-16.165
134.2513-3.51781.88518.5386-1.1792.2774-0.1272-0.69290.05771.44110.16631.10520.2736-1.4896-0.08450.5147-0.08720.20670.66740.01950.41165.5738-17.7571-3.0513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 306:312)
2X-RAY DIFFRACTION2chain 'A' and (resseq 313:332)
3X-RAY DIFFRACTION3chain 'A' and (resseq 333:376)
4X-RAY DIFFRACTION4chain 'B' and (resseq 306:312)
5X-RAY DIFFRACTION5chain 'B' and (resseq 313:327)
6X-RAY DIFFRACTION6chain 'B' and (resseq 328:332)
7X-RAY DIFFRACTION7chain 'B' and (resseq 333:346)
8X-RAY DIFFRACTION8chain 'B' and (resseq 347:359)
9X-RAY DIFFRACTION9chain 'B' and (resseq 360:370)
10X-RAY DIFFRACTION10chain 'B' and (resseq 371:376)
11X-RAY DIFFRACTION11chain 'C' and (resseq 306:312)
12X-RAY DIFFRACTION12chain 'C' and (resseq 313:370)
13X-RAY DIFFRACTION13chain 'C' and (resseq 371:376)

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