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- PDB-5nqg: Crystal structure of Plasmodium vivax AMA1 in complex with a 39 a... -

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Basic information

Entry
Database: PDB / ID: 5nqg
TitleCrystal structure of Plasmodium vivax AMA1 in complex with a 39 aa PvRON2 peptide
Components
  • Apical merozoite antigen 1
  • RON2
KeywordsCELL INVASION / AMA1 / RON2 / Malaria
Function / homologyApical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Rhoptry neck protein 2 / Apical merozoite antigen 1 / Apical merozoite antigen 1
Function and homology information
Biological speciesPLASMODIUM VIVAX SAL-1 (eukaryote)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVulliez-le Normand, B. / Saul, F.A. / Faber, B.W. / Bentley, G.A.
CitationJournal: PLoS ONE / Year: 2017
Title: Cross-reactivity between apical membrane antgen 1 and rhoptry neck protein 2 in P. vivax and P. falciparum: A structural and binding study.
Authors: Vulliez-Le Normand, B. / Saul, F.A. / Hoos, S. / Faber, B.W. / Bentley, G.A.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 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: Apical merozoite antigen 1
B: RON2


Theoretical massNumber of molelcules
Total (without water)58,5202
Polymers58,5202
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SPR analysis of binding interaction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.460, 54.000, 62.130
Angle α, β, γ (deg.)90.00, 105.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apical merozoite antigen 1


Mass: 54413.008 Da / Num. of mol.: 1 / Mutation: Q119E, S178N, N226D, N441Q
Source method: isolated from a genetically manipulated source
Details: EXPRESSION TAG: E1, A2, S3, I4 ENGINEERED MUTATIONS : Q119E, S178N, N226D, N441Q. EXPRESSION TAG: LEQKLISEEDLNSAVDHHHHHH
Source: (gene. exp.) PLASMODIUM VIVAX SAL-1 (eukaryote) / Gene: AMA1 / Production host: Komagataella pastoris (fungus) / References: UniProt: O61130, UniProt: A5K4Z2*PLUS
#2: Protein/peptide RON2


Mass: 4106.740 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: A5K3N8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 3350, sodium citrate, isopropanol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→42.5 Å / Num. obs: 28667 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Net I/σ(I): 9.6
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4162 / CC1/2: 0.698 / Rpim(I) all: 0.452 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W8K

1w8k


Resolution: 2.15→39.58 Å / Cor.coef. Fo:Fc: 0.9233 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1641 5.85 %RANDOM
Rwork0.1738 ---
obs0.1768 28038 97.33 %-
Displacement parametersBiso mean: 49.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.3253 Å20 Å212.1017 Å2
2--15.1405 Å20 Å2
3----18.4658 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: 1 / Resolution: 2.15→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 234 3558
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013408HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094610HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1212SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes489HARMONIC5
X-RAY DIFFRACTIONt_it3408HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion18.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion441SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3905SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.23 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2492 156 6.61 %
Rwork0.2288 2205 -
all0.2302 2361 -
obs--78.92 %

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