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- PDB-9evn: Plasmodium falciparum apical membrane antigen FVO -

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Basic information

Entry
Database: PDB / ID: 9evn
TitlePlasmodium falciparum apical membrane antigen FVO
ComponentsApical membrane antigen 1
KeywordsCELL INVASION / Plasmodium falciparum / Antigen / vaccine candidate / malaria
Function / homologyApical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Apical membrane antigen 1
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBentley, G.A. / Saul, F.A. / Vulliez-Le Normand, B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J Struct Biol X / Year: 2024
Title: Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1.
Authors: Saul, F.A. / Vulliez-Le Normand, B. / Boes, A. / Spiegel, H. / Kocken, C.H.M. / Faber, B.W. / Bentley, G.A.
History
DepositionMar 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2283
Polymers40,1571
Non-polymers712
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-11 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.276, 94.216, 96.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apical membrane antigen 1 / Merozoite surface antigen


Mass: 40156.828 Da / Num. of mol.: 1 / Mutation: N162K, T288V, S373D, N422D, S423K
Source method: isolated from a genetically manipulated source
Details: Residues E102, A103, E104 and F105 are non-native since they derive from the cloning of the PfAMA1-3D7 gene.
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: FVO / Gene: AMA1 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A075DBS4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Crystals of PfAMA1-FVO were obtained by mixing 1 micro-L of protein and 1 micro-L of reservoir buffer containing 35 % PEG 5000 monomethylether, 0.1M Tris pH 8.5 and 0.2M Li2SO4. The final ...Details: Crystals of PfAMA1-FVO were obtained by mixing 1 micro-L of protein and 1 micro-L of reservoir buffer containing 35 % PEG 5000 monomethylether, 0.1M Tris pH 8.5 and 0.2M Li2SO4. The final protein concentration was 3.5 mg/ml. Cryo-protecting buffer for PfAMA1-FVO crystals consisted of the crystallisation buffer with 15% of glycerol (v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→47.11 Å / Num. obs: 24245 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.994 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1754 / CC1/2: 0.491

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.705 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1225 5.1 %RANDOM
Rwork0.17675 ---
obs0.17889 22895 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0 Å2
2---0.45 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 2 256 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122695
X-RAY DIFFRACTIONr_bond_other_d0.0060.0162425
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6713653
X-RAY DIFFRACTIONr_angle_other_deg0.6511.5855615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.38859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07910447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023175
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02625
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6224.9331306
X-RAY DIFFRACTIONr_mcbond_other4.5924.9351306
X-RAY DIFFRACTIONr_mcangle_it6.7988.8981627
X-RAY DIFFRACTIONr_mcangle_other6.8068.9021628
X-RAY DIFFRACTIONr_scbond_it5.3155.4291389
X-RAY DIFFRACTIONr_scbond_other5.3135.4331390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2529.7612024
X-RAY DIFFRACTIONr_long_range_B_refined10.9351.522932
X-RAY DIFFRACTIONr_long_range_B_other10.76650.692866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 88 -
Rwork0.294 1590 -
obs--95.78 %

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