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- PDB-5ouo: Structure of TgPLP1 APCbeta domain -

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Basic information

Entry
Database: PDB / ID: 5ouo
TitleStructure of TgPLP1 APCbeta domain
ComponentsPerforin-like protein 1
KeywordsLIPID BINDING PROTEIN / Toxoplasma / cell egress / beta prism
Function / homology
Function and homology information


microneme membrane / exit from host cell / symbiont-containing vacuole membrane / wide pore channel activity / cytoplasmic vesicle / killing of cells of another organism
Similarity search - Function
membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
Perforin-like protein 1 / Perforin-like protein 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.11 Å
AuthorsNi, T. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000331/1 United Kingdom
CitationJournal: Sci Adv / Year: 2018
Title: Structures of monomeric and oligomeric forms of theToxoplasma gondiiperforin-like protein 1.
Authors: Ni, T. / Williams, S.I. / Rezelj, S. / Anderluh, G. / Harlos, K. / Stansfeld, P.J. / Gilbert, R.J.C.
History
DepositionAug 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0154
Polymers29,9311
Non-polymers843
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-21 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.760, 50.210, 52.280
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1265-

HOH

21A-1529-

HOH

31A-1625-

HOH

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Components

#1: Protein Perforin-like protein 1


Mass: 29930.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: PLP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A1E348, UniProt: V5BCL0*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.2M MgCl2, 0.1M bis-Tris, pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.1→50.37 Å / Num. obs: 99521 / % possible obs: 96.8 % / Redundancy: 6.1 % / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2044: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.11→50.37 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.1667 4822 4.85 %
Rwork0.1492 --
obs0.1501 99513 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.11→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 3 434 2411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062095
X-RAY DIFFRACTIONf_angle_d1.0822850
X-RAY DIFFRACTIONf_dihedral_angle_d14.168793
X-RAY DIFFRACTIONf_chiral_restr0.07307
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.12260.31571040.33322366X-RAY DIFFRACTION73
1.1226-1.13580.35691460.32982530X-RAY DIFFRACTION78
1.1358-1.14970.32611290.32142705X-RAY DIFFRACTION84
1.1497-1.16430.31861340.29992856X-RAY DIFFRACTION88
1.1643-1.17960.31441650.29713032X-RAY DIFFRACTION93
1.1796-1.19570.26341840.29443165X-RAY DIFFRACTION97
1.1957-1.21280.29141310.28183216X-RAY DIFFRACTION99
1.2128-1.23090.29811580.27163210X-RAY DIFFRACTION99
1.2309-1.25020.28191550.26173270X-RAY DIFFRACTION99
1.2502-1.27070.27091710.25643175X-RAY DIFFRACTION99
1.2707-1.29260.2351700.23483183X-RAY DIFFRACTION99
1.2926-1.31610.2181610.22943283X-RAY DIFFRACTION99
1.3161-1.34140.22891770.21833225X-RAY DIFFRACTION99
1.3414-1.36880.23511760.20733186X-RAY DIFFRACTION100
1.3688-1.39850.23411750.20293222X-RAY DIFFRACTION100
1.3985-1.43110.20821910.18833225X-RAY DIFFRACTION100
1.4311-1.46690.20331530.17853268X-RAY DIFFRACTION100
1.4669-1.50650.17891620.16523245X-RAY DIFFRACTION100
1.5065-1.55090.16371590.153253X-RAY DIFFRACTION100
1.5509-1.60090.16861550.1493262X-RAY DIFFRACTION100
1.6009-1.65810.17311970.14073259X-RAY DIFFRACTION100
1.6581-1.72450.16021570.14463220X-RAY DIFFRACTION99
1.7245-1.8030.17661600.14243287X-RAY DIFFRACTION100
1.803-1.89810.14741490.1283265X-RAY DIFFRACTION100
1.8981-2.0170.14291760.11563292X-RAY DIFFRACTION100
2.017-2.17270.12041700.10693256X-RAY DIFFRACTION100
2.1727-2.39140.13441630.1093266X-RAY DIFFRACTION100
2.3914-2.73740.11971690.11313288X-RAY DIFFRACTION100
2.7374-3.44870.14041640.10953303X-RAY DIFFRACTION100
3.4487-50.42490.12011610.11413378X-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)
11.1417-0.207-0.11410.9082-0.40052.49870.0033-0.0034-0.05430.00160.00290.05980.0816-0.0168-0.0120.0725-0.00410.00440.0677-0.00080.0994114.3196-56.81781.6881
22.27770.28630.19272.10350.25033.650.0396-0.0262-0.08450.0071-0.0498-0.16510.10920.1827-0.0170.05810.01180.0030.04580.00480.104127.8665-51.1776-0.3767
31.70380.1966-1.98890.5273-0.63684.66230.0625-0.15360.07820.0629-0.0086-0.0332-0.09890.1545-0.05870.0717-0.0038-0.00720.08-0.0180.0983124.6845-45.96567.499
41.3420.0324-0.69840.89590.15762.40670.1141-0.15140.2188-0.02770.0208-0.1118-0.11140.2107-0.16630.07850.00610.00220.051-0.00480.1259114.0523-40.48973.3598
51.3163-0.2272-0.78210.8593-1.24354.53840.07250.01080.17160.0282-0.00180.0267-0.1418-0.0992-0.07140.0546-0.00640.00880.0572-0.010.0978108.7986-43.04022.8241
61.8081-0.221-2.54270.08930.35746.07480.006-0.05590.07960.0310.02830.00430.0738-0.0532-0.04840.0674-0.01180.00020.0664-0.01590.0974109.1018-44.225113.6366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 810 through 890 )
2X-RAY DIFFRACTION2chain 'A' and (resid 891 through 931 )
3X-RAY DIFFRACTION3chain 'A' and (resid 932 through 972 )
4X-RAY DIFFRACTION4chain 'A' and (resid 973 through 1002 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1003 through 1046 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1047 through 1072 )

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