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- PDB-5nqf: Crystal structure of Plasmodium falciparum AMA1 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5nqf
TitleCrystal structure of Plasmodium falciparum AMA1 in complex with a 39 aa PvRON2 peptide
Components
  • Apical membrane antigen 1
  • Rhoptry neck protein 2
KeywordsCELL INVASION / AMA1 / RON2 / MALARIA
Function / homology
Function and homology information


Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum Vietnam Oak-Knoll (eukaryote)
Plasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1
B: Rhoptry neck protein 2


Theoretical massNumber of molelcules
Total (without water)46,7972
Polymers46,7972
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SPR analysis of binding interaction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-22 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.481, 38.248, 72.356
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apical membrane antigen 1


Mass: 42690.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 97-442 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES I97-P442 OF PFAMA1-FVO. N-TERMINAL STRETCH EF IS A CLONING ARTEFACT. C-TERMINAL STRETCH GLEQKLISEEDLNSAVDHHHHHH IS AN EXPRESSION TAG ( C-MYC + HEXA-HIS ). N162K, T288V, S373D, ...Details: RESIDUES I97-P442 OF PFAMA1-FVO. N-TERMINAL STRETCH EF IS A CLONING ARTEFACT. C-TERMINAL STRETCH GLEQKLISEEDLNSAVDHHHHHH IS AN EXPRESSION TAG ( C-MYC + HEXA-HIS ). N162K, T288V, S373D, N422D, S423K ARE ENGINEERED MUTATIONS.
Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote)
Gene: PFFVO_05649 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A024UZE1
#2: Protein/peptide Rhoptry neck protein 2


Mass: 4106.740 Da / Num. of mol.: 1 / Fragment: UNP Residues 2034-2072 / Source method: obtained synthetically / Source: (synth.) Plasmodium vivax Sal-1 (eukaryote) / References: UniProt: A5K3N8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 3350, TRIS 8.2, SODIUM ACETATE, ISOPROPANOL, PH 8.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
PH range: 8.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91165 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.9→46.92 Å / Num. obs: 29741 / % possible obs: 96.2 % / Redundancy: 3 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.822 / % possible all: 78.3

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMA1-FVO

Resolution: 1.9→35.78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1511 5.08 %RANDOM
Rwork0.169 ---
obs0.171 29729 95.9 %-
Displacement parametersBiso mean: 28.57 Å2
Baniso -1Baniso -2Baniso -3
1--6.3093 Å20 Å20.3143 Å2
2---0.3694 Å20 Å2
3---6.6786 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 0 307 2933
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012738HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043720HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d930SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes391HARMONIC5
X-RAY DIFFRACTIONt_it2738HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion18.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion350SEMIHARMONIC5
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_contact3319SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2946 113 5.17 %
Rwork0.2331 2073 -
all0.2363 2186 -
obs--72.84 %

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