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- PDB-5tsz: Crystal structure of Plasmodium vivax CelTOS -

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Basic information

Entry
Database: PDB / ID: 5tsz
TitleCrystal structure of Plasmodium vivax CelTOS
ComponentsPv cell-traversal protein
KeywordsCELL INVASION / membrane disruption / pore / malaria / traversal
Function / homologyCell-traversal protein for ookinetes and sporozoites / Cell-traversal protein for ookinetes and sporozoites / Cell traversal protein of ookinetes and sporozoites
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.002 Å
AuthorsTolia, N.H. / Jimah, J.R.
CitationJournal: Elife / Year: 2016
Title: Malaria parasite CelTOS targets the inner leaflet of cell membranes for pore-dependent disruption.
Authors: Jimah, J.R. / Salinas, N.D. / Sala-Rabanal, M. / Jones, N.G. / Sibley, L.D. / Nichols, C.G. / Schlesinger, P.H. / Tolia, N.H.
History
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pv cell-traversal protein
B: Pv cell-traversal protein
C: Pv cell-traversal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1326
Polymers56,0633
Non-polymers693
Water1629
1
A: Pv cell-traversal protein
B: Pv cell-traversal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4214
Polymers37,3752
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-61 kcal/mol
Surface area14510 Å2
MethodPISA
2
C: Pv cell-traversal protein
hetero molecules

C: Pv cell-traversal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4214
Polymers37,3752
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y,x,-z-11
Buried area3210 Å2
ΔGint-57 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.960, 158.960, 64.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pv cell-traversal protein


Mass: 18687.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: pvCelTOS / Production host: Escherichia coli (E. coli) / References: UniProt: Q53UB7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.6 M Ammonium dihydrogen phosphate, 0.08 M Tris pH 8.5 and 20% glycerol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 18, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 18263 / % possible obs: 96.6 % / Redundancy: 5 % / Rsym value: 0.096 / Net I/σ(I): 14.86
Reflection shellHighest resolution: 3 Å / Rsym value: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementResolution: 3.002→19.762 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2378 946 5.2 %
Rwork0.2197 --
obs0.2207 18208 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.002→19.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 3 9 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073057
X-RAY DIFFRACTIONf_angle_d0.694101
X-RAY DIFFRACTIONf_dihedral_angle_d12.0571863
X-RAY DIFFRACTIONf_chiral_restr0.037492
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0024-3.16010.35841230.31712412X-RAY DIFFRACTION97
3.1601-3.35710.30111330.2852524X-RAY DIFFRACTION99
3.3571-3.61490.25591520.24352442X-RAY DIFFRACTION98
3.6149-3.9760.23811500.2252460X-RAY DIFFRACTION98
3.976-4.54520.24341450.20212463X-RAY DIFFRACTION97
4.5452-5.70360.22551200.20732486X-RAY DIFFRACTION97
5.7036-19.76280.18891230.18862475X-RAY DIFFRACTION94

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