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

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Basic information

Entry
Database: PDB / ID: 5oup
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 / wide pore channel activity / cytoplasmic vesicle / killing of cells of another organism
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 / SIRAS / Resolution: 2.03 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 1.1Apr 18, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2May 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 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)39,3342
Polymers39,1131
Non-polymers2211
Water1,76598
1
A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules

A: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,33814
Polymers273,7897
Non-polymers1,5487
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
crystal symmetry operation3_554-x+y,-x,z-2/31
crystal symmetry operation4_554-x,-y,z-1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation5_554y,-x+y,z-5/61
crystal symmetry operation6_554x-y,x,z-1/61
Unit cell
Length a, b, c (Å)104.860, 104.860, 52.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Perforin-like protein 1


Mass: 39112.723 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: G3G7T1, UniProt: V5BCL0*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.5, 10% isopropanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.0719 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 2.03→90.81 Å / Num. obs: 21264 / % possible obs: 100 % / Redundancy: 13.4 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.03→52.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.68
RfactorNum. reflection% reflection
Rfree0.2325 965 4.54 %
Rwork0.1913 --
obs0.193 21265 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→52.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 14 98 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022210
X-RAY DIFFRACTIONf_angle_d0.573003
X-RAY DIFFRACTIONf_dihedral_angle_d16.2031320
X-RAY DIFFRACTIONf_chiral_restr0.045328
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0302-2.13730.26181560.25172877X-RAY DIFFRACTION100
2.1373-2.27120.28541380.24022866X-RAY DIFFRACTION100
2.2712-2.44650.26011530.25192852X-RAY DIFFRACTION100
2.4465-2.69270.27811220.22022913X-RAY DIFFRACTION100
2.6927-3.08230.28861430.20712894X-RAY DIFFRACTION100
3.0823-3.88320.21971230.16922917X-RAY DIFFRACTION100
3.8832-52.44750.18591300.16622981X-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)
12.4227-0.7176-0.25062.80371.27441.4458-0.085-0.2209-0.29120.270.01880.19050.0908-0.02210.05920.30520.0157-0.03110.2901-0.01050.2968-22.925329.66975.97
22.80780.6239-1.18571.9203-0.66472.6142-0.2415-0.24890.0923-0.0318-0.00490.31820.2401-0.04850.22130.3124-0.0323-0.04580.2824-0.09130.3649-22.675115.4607-1.6571
34.0694-1.088-1.27923.9555-0.08982.9789-0.05080.28860.2055-0.3006-0.1098-0.3829-0.19030.04160.09480.3193-0.0097-0.04560.27940.0140.2813-10.327231.2204-8.3214
47.1086-0.1387-2.07242.19820.95782.1796-0.01360.2178-0.00110.0022-0.19260.1337-0.0251-0.13660.27540.26190.0421-0.06910.3257-0.03420.2248-15.022118.8242-3.0633
54.63970.0188-0.83163.0423-0.95934.04640.1070.06550.56820.0856-0.0506-0.1845-0.9291-0.0693-0.04940.6570.0997-0.04250.3054-0.06170.3692-22.973350.04482.8618
66.4774-1.0027-0.8181.7519-0.5023.1197-0.0843-0.5466-0.4390.1023-0.1441-0.22560.08880.4380.02170.2401-0.0396-0.05320.2436-0.0250.2834-7.822220.45160.5839
74.1147-0.2967-0.65824.7836-0.95882.51520.01330.02-0.33780.0286-0.1551-0.0717-0.0846-0.16530.0560.24110.0147-0.02550.254-0.04720.2025-21.309433.67560.511
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 537 )
3X-RAY DIFFRACTION3chain 'A' and (resid 538 through 581 )
4X-RAY DIFFRACTION4chain 'A' and (resid 582 through 598 )
5X-RAY DIFFRACTION5chain 'A' and (resid 599 through 663 )
6X-RAY DIFFRACTION6chain 'A' and (resid 664 through 747 )
7X-RAY DIFFRACTION7chain 'A' and (resid 748 through 800 )

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