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- PDB-5own: Structure of TgPLP1 MACPF domain -

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Basic information

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


microneme membrane / exit from host cell / symbiont-containing vacuole membrane / membrane attack complex / wide pore channel activity / complement activation / cytoplasmic vesicle / killing of cells of another organism / extracellular space
Similarity search - Function
membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / 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 / MOLECULAR REPLACEMENT / Resolution: 3.11 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
DepositionSep 1, 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
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)78,4473
Polymers78,2252
Non-polymers2211
Water00
1
A: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3342
Polymers39,1131
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Perforin-like protein 1


Theoretical massNumber of molelcules
Total (without water)39,1131
Polymers39,1131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.230, 206.580, 82.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Perforin-like protein 1


Mass: 39112.723 Da / Num. of mol.: 2
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: G3G7T1, UniProt: V5BCL0*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dihydrate, pH 5.5, 22% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.11→64.58 Å / Num. obs: 15082 / % possible obs: 100 % / Redundancy: 31.9 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OUO

5ouo


Resolution: 3.11→55.8 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.98
RfactorNum. reflection% reflection
Rfree0.2617 753 4.99 %
Rwork0.2349 --
obs0.2363 15082 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.11→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 14 0 4566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034671
X-RAY DIFFRACTIONf_angle_d0.6916332
X-RAY DIFFRACTIONf_dihedral_angle_d13.6422818
X-RAY DIFFRACTIONf_chiral_restr0.043692
X-RAY DIFFRACTIONf_plane_restr0.004825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1101-3.35020.42161520.36882827X-RAY DIFFRACTION100
3.3502-3.68730.29881280.27792833X-RAY DIFFRACTION100
3.6873-4.22070.26581490.23472834X-RAY DIFFRACTION100
4.2207-5.31690.20661590.19832855X-RAY DIFFRACTION100
5.3169-55.80930.25671650.21832980X-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)
18.0016-0.9208-0.00778.83760.85894.2619-0.2429-0.11740.45110.22850.5526-1.72710.08180.2757-0.31820.5748-0.1558-0.0140.60.03270.8947-25.9288-31.8696-13.5546
27.0414-1.9302-3.88013.55411.3473.7818-0.36580.92050.756-0.23230.0187-0.04480.205-0.55780.28950.6764-0.1768-0.14680.70210.14130.7936-31.3405-23.7041-23.2157
32.51740.6123-0.44212.93274.35547.2365-0.5802-0.25190.59330.57190.80651.8105-1.66440.3355-0.15781.02530.1354-0.25710.9687-0.15522.0143-40.7464-10.4155-11.549
45.14610.8473-1.10254.2893-1.24322.0467-0.2691-0.26220.1820.06460.17240.10950.23770.05710.15120.5734-0.0979-0.05040.5568-0.02840.6149-34.9392-34.3257-14.2464
53.2-0.1781-1.48133.73451.36373.8768-0.13220.08830.71850.20150.27050.07790.1043-0.4288-0.18420.38220.008-0.12410.60170.09210.9196-37.9093-23.483-10.801
69.4708-6.05625.75399.8137-3.92528.26-0.6804-0.55711.20170.1961.0391-0.9273-0.8265-0.7259-0.37890.6219-0.07970.05730.7190.01151.4947-25.0524-6.5609-18.879
77.37861.4278-1.34554.9153-3.47323.6024-0.2610.1621-0.22970.29720.2502-0.33720.3462-0.0854-0.0240.6833-0.0150.06550.4983-0.05590.8195-32.792-31.269-14.4628
87.8805-0.43984.43499.3433-3.06476.43230.0188-0.09640.3541-0.6196-0.02650.98220.3636-0.1013-0.07740.5492-0.0363-0.01750.59060.01980.6327-8.8627-22.9805-3.2223
97.92910.8358-2.33017.56110.46124.80850.0149-0.86560.67210.2388-0.2081-0.22860.35260.49170.22190.65130.0927-0.19150.8922-0.15370.4865.6136-21.60882.7042
108.71071.2886-0.41378.67990.23.8231-0.23850.0522-0.709-0.85930.0141-0.79130.60210.34150.1950.91060.0095-0.03990.57210.14160.7848-13.5192-42.0989-1.2805
114.85121.25431.03183.5476-0.66232.3890.11980.1265-0.03860.1609-0.1345-0.81160.2451.2047-0.060.63580.1156-0.07861.0447-0.18531.055915.7972-17.62590.1684
126.35791.8848-0.41624.9289-0.94243.2712-0.1931-0.013-0.1352-0.01520.16440.30650.1880.2879-0.0940.5580.2068-0.08130.7254-0.05240.5513-5.1937-25.4087-0.6566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 465 through 517 )
2X-RAY DIFFRACTION2chain 'A' and (resid 518 through 567 )
3X-RAY DIFFRACTION3chain 'A' and (resid 568 through 581 )
4X-RAY DIFFRACTION4chain 'A' and (resid 582 through 633 )
5X-RAY DIFFRACTION5chain 'A' and (resid 634 through 692 )
6X-RAY DIFFRACTION6chain 'A' and (resid 693 through 747 )
7X-RAY DIFFRACTION7chain 'A' and (resid 748 through 799 )
8X-RAY DIFFRACTION8chain 'B' and (resid 464 through 519 )
9X-RAY DIFFRACTION9chain 'B' and (resid 520 through 597 )
10X-RAY DIFFRACTION10chain 'B' and (resid 598 through 663 )
11X-RAY DIFFRACTION11chain 'B' and (resid 664 through 737 )
12X-RAY DIFFRACTION12chain 'B' and (resid 738 through 799 )

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