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- PDB-9dx6: Crystal structure of Plasmodium vivax (Palo Alto) PvAMA1 in compl... -

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Basic information

Entry
Database: PDB / ID: 9dx6
TitleCrystal structure of Plasmodium vivax (Palo Alto) PvAMA1 in complex with human Fab 826827
Components
  • 826827 Fab Heavy chain
  • 826827 Fab Light chain
  • Apical merozoite protein 1
KeywordsCELL INVASION / inhibitory antibody / complex / Plasmodium vivax
Function / homologyApical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Apical merozoite protein 1
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDietrich, M.H. / Tham, W.H. / Jung, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI143694 United States
Department of Veterans Affairs (VA, United States)BX001350 United States
CitationJournal: Nat Commun / Year: 2024
Title: Potent AMA1-specific human monoclonal antibody against Plasmodium vivax Pre-erythrocytic and Blood Stages.
Authors: Winnicki, A.C. / Dietrich, M.H. / Yeoh, L.M. / Carias, L.L. / Roobsoong, W. / Drago, C.L. / Malachin, A.N. / Redinger, K.R. / Feufack-Donfack, L.B. / Baldor, L. / Jung, N.C. / McLaine, O.S. ...Authors: Winnicki, A.C. / Dietrich, M.H. / Yeoh, L.M. / Carias, L.L. / Roobsoong, W. / Drago, C.L. / Malachin, A.N. / Redinger, K.R. / Feufack-Donfack, L.B. / Baldor, L. / Jung, N.C. / McLaine, O.S. / Skomorovska-Prokvolit, Y. / Orban, A. / Opi, D.H. / Kirtley, P. / Nielson, K. / Aleshnick, M. / Zanghi, G. / Rezakhani, N. / Vaughan, A.M. / Wilder, B.K. / Sattabongkot, J. / Tham, W.H. / Popovici, J. / Beeson, J.G. / Bosch, J. / King, C.L.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical merozoite protein 1
B: 826827 Fab Heavy chain
C: 826827 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)102,8993
Polymers102,8993
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-39 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.237, 54.461, 104.130
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apical merozoite protein 1


Mass: 54376.090 Da / Num. of mol.: 1 / Mutation: S178N, N226D, N441Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: ama1 / Production host: Homo sapiens (human) / References: UniProt: B9TXF7
#2: Antibody 826827 Fab Heavy chain


Mass: 24953.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 826827 Fab Light chain


Mass: 23569.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG Smear Broad, 0.1 M Tris pH 8.5, 0.3 M Glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724563122 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724563122 Å / Relative weight: 1
ReflectionResolution: 2.4→47.76 Å / Num. obs: 41378 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.18 / Net I/σ(I): 9.53
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.4-2.541.08666140.6421.1761
2.54-2.720.74362290.7920.81
2.72-2.930.49357850.90.5311
2.93-3.210.30653770.9540.3311
3.21-3.590.1748810.9850.1841
3.59-4.140.10742840.9940.1151
4.14-5.060.07436520.9970.0791
5.06-7.120.07928770.9960.0861

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.76 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2060 5 %
Rwork0.1915 --
obs0.1936 41218 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 0 259 6654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046543
X-RAY DIFFRACTIONf_angle_d0.6688894
X-RAY DIFFRACTIONf_dihedral_angle_d5.854901
X-RAY DIFFRACTIONf_chiral_restr0.045983
X-RAY DIFFRACTIONf_plane_restr0.0061162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.3551360.29732579X-RAY DIFFRACTION100
2.46-2.520.31171370.27682589X-RAY DIFFRACTION100
2.52-2.590.30431360.25252598X-RAY DIFFRACTION100
2.59-2.660.28711350.23552564X-RAY DIFFRACTION100
2.66-2.750.3211370.2272609X-RAY DIFFRACTION100
2.75-2.850.28571360.22512592X-RAY DIFFRACTION100
2.85-2.960.24081370.20672597X-RAY DIFFRACTION100
2.96-3.090.25871360.19462594X-RAY DIFFRACTION100
3.09-3.260.23591370.18762607X-RAY DIFFRACTION100
3.26-3.460.2221370.17892601X-RAY DIFFRACTION100
3.46-3.730.21471370.17532600X-RAY DIFFRACTION100
3.73-4.10.19791380.16452612X-RAY DIFFRACTION100
4.1-4.70.19351390.15972641X-RAY DIFFRACTION100
4.7-5.920.22161390.18272644X-RAY DIFFRACTION100
5.92-47.760.23341430.1952731X-RAY DIFFRACTION100

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