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- PDB-9evo: Plasmodium falciparum apical membrane antigen 3D7 -

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Basic information

Entry
Database: PDB / ID: 9evo
TitlePlasmodium falciparum apical membrane antigen 3D7
ComponentsApical membrane antigen 1
KeywordsCELL INVASION / Plasmodium falciparum / Antigen / vaccine candidate / malaria
Function / homology
Function and homology information


apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Domain/homology
Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
B: Apical membrane antigen 1


Theoretical massNumber of molelcules
Total (without water)82,9992
Polymers82,9992
Non-polymers00
Water5,801322
1
A: Apical membrane antigen 1


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apical membrane antigen 1


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.230, 62.060, 71.500
Angle α, β, γ (deg.)89.13, 89.90, 83.92
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 41499.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutations for potential N-glycosylation sites: T164A, T288A, S373A, S423A, S424A
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: PF3D7_1133400 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q7KQK5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Crystals of PfAMA1-3D7 were obtained by mixing 1.2 micro-L of protein and 1.2 micro-L of reservoir buffer containing 12% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2. The final protein ...Details: Crystals of PfAMA1-3D7 were obtained by mixing 1.2 micro-L of protein and 1.2 micro-L of reservoir buffer containing 12% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2. The final protein concentration was 3.5 mg/ml. Before mounting, 1 micro-L of a 20mM solution of a small molecule NCGC00015280 (demonstrated as inhibiting the AMA1-RON2 interaction and referenced as B43 in the PDB), was dissolved in DMSO and half diluted with the reservoir buffer, then added to the drop containing the crystals. Cryo-protecting buffer for the PfAMA1-3D7 crystals consisted of 90% of reservoir buffer containing 20% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2 supplemented with 10% glycerol, and 10% of a 20mM solution of B43.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→47.06 Å / Num. obs: 37352 / % possible obs: 97.9 % / Redundancy: 2 % / CC1/2: 0.902 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.179 / Rrim(I) all: 0.268 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5400 / CC1/2: 0.215 / Rpim(I) all: 0.795 / Rrim(I) all: 1.183

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.37 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.722 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25599 1908 5.1 %RANDOM
Rwork0.20732 ---
obs0.20977 35400 97.77 %-
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: 26.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.47 Å20.23 Å2
2--1.48 Å2-1.01 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 0 322 5100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124913
X-RAY DIFFRACTIONr_bond_other_d0.0050.0164417
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.676676
X-RAY DIFFRACTIONr_angle_other_deg0.7271.58510213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.741512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34610779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025760
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021104
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_it2.3052.8262430
X-RAY DIFFRACTIONr_mcbond_other2.3042.8262430
X-RAY DIFFRACTIONr_mcangle_it3.7195.0793024
X-RAY DIFFRACTIONr_mcangle_other3.7185.083025
X-RAY DIFFRACTIONr_scbond_it2.4393.0312483
X-RAY DIFFRACTIONr_scbond_other2.4393.0332484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0545.4853652
X-RAY DIFFRACTIONr_long_range_B_refined6.03728.035327
X-RAY DIFFRACTIONr_long_range_B_other5.99227.895269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 136 -
Rwork0.273 2560 -
obs--95.67 %

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