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- PDB-6d7a: Structure of T. gondii PLP1 beta-rich domain -

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Basic information

Entry
Database: PDB / ID: 6d7a
TitleStructure of T. gondii PLP1 beta-rich domain
ComponentsPerforin-like protein 1
KeywordsLIPID BINDING PROTEIN / Pore forming protein / toxin / perforin-like protein / beta-prism
Function / homologymembrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Perforin-like protein 1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.13 Å
AuthorsGuerra, A.J. / Koropatkin, N.M. / Wawrzak, Z. / Bahr, C.M.E. / Carruthers, V.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI046675 United States
CitationJournal: PLoS Pathog. / Year: 2018
Title: Structural basis of Toxoplasma gondii perforin-like protein 1 membrane interaction and activity during egress.
Authors: Guerra, A.J. / Zhang, O. / Bahr, C.M.E. / Huynh, M.H. / DelProposto, J. / Brown, W.C. / Wawrzak, Z. / Koropatkin, N.M. / Carruthers, V.B.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Perforin-like protein 1
B: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2126
Polymers76,1202
Non-polymers924
Water11,782654
1
A: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1063
Polymers38,0601
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1063
Polymers38,0601
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.980, 50.850, 105.340
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1616-

HOH

21B-1610-

HOH

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Components

#1: Protein Perforin-like protein 1


Mass: 38060.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: PLP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1E348
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 1.79 Å3/Da / Density % sol: 31.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 0.8M sodium formate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 25, 2016 / Details: Be lens
RadiationMonochromator: C(111) diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.13→24.883 Å / Num. obs: 191300 / % possible obs: 94.92 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07709 / Rpim(I) all: 0.03364 / Rrim(I) all: 0.08447 / Net I/σ(I): 7.99
Reflection shellResolution: 1.13→1.17 Å

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.13→24.883 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1637 9505 4.97 %
Rwork0.1407 --
obs0.1418 191287 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.13→24.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 4 654 4638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094248
X-RAY DIFFRACTIONf_angle_d1.0445808
X-RAY DIFFRACTIONf_dihedral_angle_d15.5071634
X-RAY DIFFRACTIONf_chiral_restr0.089638
X-RAY DIFFRACTIONf_plane_restr0.007772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.14280.33032230.31024170X-RAY DIFFRACTION66
1.1428-1.15630.3062470.29864450X-RAY DIFFRACTION70
1.1563-1.17040.2732670.29834888X-RAY DIFFRACTION78
1.1704-1.18520.28683090.27525395X-RAY DIFFRACTION84
1.1852-1.20080.28942920.24895746X-RAY DIFFRACTION91
1.2008-1.21720.27463730.22756045X-RAY DIFFRACTION96
1.2172-1.23460.2363290.21626097X-RAY DIFFRACTION96
1.2346-1.25310.22843520.19916112X-RAY DIFFRACTION97
1.2531-1.27260.22373060.1816304X-RAY DIFFRACTION98
1.2726-1.29350.20623270.17026216X-RAY DIFFRACTION98
1.2935-1.31580.21283050.16686194X-RAY DIFFRACTION98
1.3158-1.33970.18813330.15326229X-RAY DIFFRACTION98
1.3397-1.36550.18523220.14446242X-RAY DIFFRACTION98
1.3655-1.39340.17223630.13766276X-RAY DIFFRACTION98
1.3934-1.42370.17063010.13126280X-RAY DIFFRACTION98
1.4237-1.45680.15893240.12316291X-RAY DIFFRACTION99
1.4568-1.49320.1473300.12416269X-RAY DIFFRACTION99
1.4932-1.53360.14543270.1116316X-RAY DIFFRACTION99
1.5336-1.57870.13362830.10376324X-RAY DIFFRACTION99
1.5787-1.62960.13333550.1086331X-RAY DIFFRACTION99
1.6296-1.68790.12893430.1116290X-RAY DIFFRACTION99
1.6879-1.75540.14333470.11446310X-RAY DIFFRACTION99
1.7554-1.83530.13713200.11926437X-RAY DIFFRACTION100
1.8353-1.9320.15173610.11426280X-RAY DIFFRACTION100
1.932-2.0530.13063070.11266407X-RAY DIFFRACTION99
2.053-2.21150.13373080.11186424X-RAY DIFFRACTION100
2.2115-2.43380.13463780.11856332X-RAY DIFFRACTION100
2.4338-2.78560.14742960.12776468X-RAY DIFFRACTION100
2.7856-3.5080.15272960.1396423X-RAY DIFFRACTION99
3.508-24.88850.16232810.14776236X-RAY DIFFRACTION94

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