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- PDB-7pln: Structure of the APCbeta domain of Plasmodium vivax perforin-like... -

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Basic information

Entry
Database: PDB / ID: 7pln
TitleStructure of the APCbeta domain of Plasmodium vivax perforin-like protein 1
ComponentsSporozoite micronemal protein essential for cell traversal, putative
KeywordsCELL INVASION / Membrane binding domain / beta prism fold / APCbeta fold
Function / homologymembrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Sporozoite micronemal protein essential for cell traversal, putative
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsWilliams, S.I. / Ni, T. / Yu, X. / Gilbert, R.J.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N000331/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural, Functional and Computational Studies of Membrane Recognition by Plasmodium Perforin-Like Proteins 1 and 2
Authors: Williams, S.I. / Yu, X. / Ni, T. / Gilbert, R.J. / Stansfeld, P.J.
History
DepositionAug 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sporozoite micronemal protein essential for cell traversal, putative
B: Sporozoite micronemal protein essential for cell traversal, putative


Theoretical massNumber of molelcules
Total (without water)59,5692
Polymers59,5692
Non-polymers00
Water00
1
A: Sporozoite micronemal protein essential for cell traversal, putative


Theoretical massNumber of molelcules
Total (without water)29,7851
Polymers29,7851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sporozoite micronemal protein essential for cell traversal, putative


Theoretical massNumber of molelcules
Total (without water)29,7851
Polymers29,7851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.740, 42.020, 87.220
Angle α, β, γ (deg.)90.000, 104.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Sporozoite micronemal protein essential for cell traversal, putative


Mass: 29784.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PvPLP1 APCbeta domain polypeptide
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_030012400, PVT01_030012800 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A1G4H7E1
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Tri-potassium citrate / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.15→63.01 Å / Num. obs: 9099 / % possible obs: 98.39 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Biso Wilson estimate: 85.93 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1942 / Rpim(I) all: 0.04997 / Rrim(I) all: 0.291 / Net I/σ(I): 11.32
Reflection shellResolution: 3.15→3.263 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5668 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 790 / CC1/2: 0.695 / CC star: 0.906 / Rpim(I) all: 0.371 / % possible all: 84.67

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5OUO

5ouo


Resolution: 3.15→63.01 Å / SU ML: 0.4818 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 431 4.74 %
Rwork0.2124 8666 -
obs0.2153 9097 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.11 Å2
Refinement stepCycle: LAST / Resolution: 3.15→63.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 0 0 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01183765
X-RAY DIFFRACTIONf_angle_d1.42495111
X-RAY DIFFRACTIONf_chiral_restr0.0711591
X-RAY DIFFRACTIONf_plane_restr0.0108641
X-RAY DIFFRACTIONf_dihedral_angle_d8.6432504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.610.3661440.27162741X-RAY DIFFRACTION95.18
3.61-4.540.29241540.21752897X-RAY DIFFRACTION99.97
4.54-63.010.22191330.19133028X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.900807212513 Å / Origin y: 14.6180109927 Å / Origin z: -22.3290329102 Å
111213212223313233
T0.634846333779 Å20.0381663839748 Å20.038724018269 Å2-0.477106230195 Å20.0298981180081 Å2--0.434494369935 Å2
L7.39433767734 °21.17560137353 °20.851209045819 °2-1.29549029403 °20.167835677462 °2--1.45389810242 °2
S-0.0701087670743 Å °0.224732404878 Å °0.00202032609607 Å °0.0137284401838 Å °0.026121134769 Å °-0.0672149559488 Å °-0.00397353481644 Å °-0.17621267296 Å °0.0730034015582 Å °
Refinement TLS groupSelection details: all

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