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- PDB-6n87: Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound ... -

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Basic information

Entry
Database: PDB / ID: 6n87
TitlePlasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound to MTSL spin-labelled cyclised RON2 peptide
Components
  • Apical membrane antigen-1
  • backbone-cyclised peptide bcRON2hp
KeywordsPEPTIDE BINDING PROTEIN / AMA1 / apical membrane antigen 1 / malaria / RON2 / paramagnetic probe
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
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
Chem-MTN / Apical membrane antigen-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.588 Å
AuthorsMcGowan, S. / Drinkwater, N.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1098884 Australia
CitationJournal: ChemMedChem / Year: 2019
Title: Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe.
Authors: Akter, M. / Drinkwater, N. / Devine, S.M. / Drew, S.C. / Krishnarjuna, B. / Debono, C.O. / Wang, G. / Scanlon, M.J. / Scammells, P.J. / McGowan, S. / MacRaild, C.A. / Norton, R.S.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apical membrane antigen-1
C: backbone-cyclised peptide bcRON2hp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2043
Polymers39,9402
Non-polymers2641
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.567, 37.755, 142.176
Angle α, β, γ (deg.)90.00, 94.13, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Apical membrane antigen-1


Mass: 38390.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ama-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DI+DII / References: UniProt: Q1PBJ5
#2: Protein/peptide backbone-cyclised peptide bcRON2hp


Mass: 1548.870 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
#3: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15-20% PEG400, 0.1 M Tris pH 8.4, 20% isopropanol, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.588→40.79 Å / Num. obs: 51482 / % possible obs: 99.57 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rpim(I) all: 0.056 / Net I/σ(I): 8.62
Reflection shellResolution: 1.588→1.644 Å / Num. unique obs: 4902 / CC1/2: 0.493 / Rpim(I) all: 0.569

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1A

4r1a


Resolution: 1.588→40.787 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79
RfactorNum. reflection% reflection
Rfree0.1882 2441 4.74 %
Rwork0.1604 --
obs0.1617 51478 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.588→40.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 12 331 2890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162659
X-RAY DIFFRACTIONf_angle_d1.3873623
X-RAY DIFFRACTIONf_dihedral_angle_d5.2492147
X-RAY DIFFRACTIONf_chiral_restr0.092378
X-RAY DIFFRACTIONf_plane_restr0.01476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5877-1.62010.31881360.28892666X-RAY DIFFRACTION93
1.6201-1.65540.23541530.23712873X-RAY DIFFRACTION100
1.6554-1.69390.25361470.21242834X-RAY DIFFRACTION100
1.6939-1.73620.21721440.20182875X-RAY DIFFRACTION100
1.7362-1.78320.24081650.19242864X-RAY DIFFRACTION100
1.7832-1.83560.23951260.17462886X-RAY DIFFRACTION100
1.8356-1.89490.19441550.17072883X-RAY DIFFRACTION100
1.8949-1.96260.19331440.16562863X-RAY DIFFRACTION100
1.9626-2.04120.19731290.14782911X-RAY DIFFRACTION100
2.0412-2.13410.1731510.14792855X-RAY DIFFRACTION100
2.1341-2.24660.17261590.14052879X-RAY DIFFRACTION100
2.2466-2.38730.14961640.14052898X-RAY DIFFRACTION100
2.3873-2.57160.20641320.14762890X-RAY DIFFRACTION100
2.5716-2.83040.1721330.15742925X-RAY DIFFRACTION100
2.8304-3.23980.18981420.15392921X-RAY DIFFRACTION100
3.2398-4.08120.16231180.14262969X-RAY DIFFRACTION100
4.0812-40.80090.17521430.15833045X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 71.3163 Å / Origin y: 8.0583 Å / Origin z: 25.549 Å
111213212223313233
T0.1016 Å2-0.0036 Å2-0.0121 Å2-0.0726 Å2-0.0037 Å2--0.0939 Å2
L1.5241 °20.0523 °2-0.2439 °2-0.4286 °2-0.1849 °2--0.603 °2
S-0.0181 Å °0.1729 Å °0.0501 Å °-0.069 Å °0.0152 Å °0.0123 Å °0.0119 Å °0.0233 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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