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- PDB-7s7r: Plasmodium falciparum protein Pf12 bound to nanobody G7 -

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Basic information

Entry
Database: PDB / ID: 7s7r
TitlePlasmodium falciparum protein Pf12 bound to nanobody G7
Components
  • Merozoite surface protein P12
  • Nanobody G7
KeywordsUNKNOWN FUNCTION / 6-cysteine protein / s48/45 domain / complex / nanobody
Function / homology
Function and homology information


symbiont-containing vacuolar space / symbiont entry into host / side of membrane / apical part of cell / cell surface / plasma membrane
Similarity search - Function
6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain
Similarity search - Domain/homology
THIOCYANATE ION / Merozoite surface protein P12
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: FEMS Microbes / Year: 2022
Title: Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins.
Authors: Dietrich, M.H. / Chan, L.J. / Adair, A. / Boulet, C. / O'Neill, M.T. / Tan, L.L. / Keremane, S. / Mok, Y.F. / Lo, A.W. / Gilson, P. / Tham, W.H.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Merozoite surface protein P12
B: Nanobody G7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9266
Polymers45,5652
Non-polymers3604
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Affinity determination using Bio-layer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.931, 50.931, 322.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein Merozoite surface protein P12


Mass: 31742.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF12, PFF0615c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KSX0
#2: Antibody Nanobody G7


Mass: 13823.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: 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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Non-polymers , 3 types, 215 molecules

#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG 4000, 200 mM potassium thiocyanate, 0.05 M sodium cacodylate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→46.109 Å / Num. obs: 48590 / % possible obs: 98.7 % / Redundancy: 15.241 % / Biso Wilson estimate: 39.849 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Χ2: 0.861 / Net I/σ(I): 22.05 / Num. measured all: 740569
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.77-1.8815.9091.1171.84123886779477870.9351.15499.9
1.88-2.0115.7210.5863.88109511731269660.980.60695.3
2.01-2.1715.1760.3236.67103731683568350.9920.334100
2.17-2.3715.4720.22110.9194102633560820.9950.22896
2.37-2.6515.9290.13317.7892563581158110.9990.138100
2.65-3.0614.8310.0830.5175784511051100.9990.083100
3.06-3.7414.5590.04854.8164018440243970.9990.0599.9
3.74-5.2714.1430.03674.06493023487348610.037100
5.27-46.10913.0780.02975.36276722120211610.0399.8

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMO, 7KJH

2ymo

7kjh


Resolution: 1.77→38.703 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2419 5 %
Rwork0.2206 45997 -
obs0.2223 48416 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.9 Å2 / Biso mean: 42.4517 Å2 / Biso min: 21.95 Å2
Refinement stepCycle: final / Resolution: 1.77→38.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 21 212 3227
Biso mean--61.09 44.86 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123139
X-RAY DIFFRACTIONf_angle_d1.2144260
X-RAY DIFFRACTIONf_dihedral_angle_d4.6782556
X-RAY DIFFRACTIONf_chiral_restr0.075478
X-RAY DIFFRACTIONf_plane_restr0.008550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.77-1.80620.46831400.3878266499
1.8062-1.84540.44981410.33632666100
1.8454-1.88840.36691430.29482710100
1.8884-1.93560.49621200.4231231387
1.9356-1.98790.30371410.26972688100
1.9879-2.04640.28181410.2499271399
2.0464-2.11250.33561420.2492695100
2.1125-2.1880.2931410.24392677100
2.188-2.27560.36911300.2933245991
2.2756-2.37910.28891440.23832728100
2.3791-2.50450.29091430.25242729100
2.5045-2.66140.28311460.23652760100
2.6614-2.86680.30381450.24032754100
2.8668-3.15520.25991470.23532790100
3.1552-3.61150.25051460.20312774100
3.6115-4.54890.18911490.17612829100
4.5489-38.70.20991600.18833048100

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