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- PDB-6n7q: Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound ... -

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Basic information

Entry
Database: PDB / ID: 6n7q
TitlePlasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound to cyclised RON2 peptide
Components
  • Apical membrane antigen-1
  • RON2 peptide
KeywordsPEPTIDE BINDING PROTEIN / AMA1 / apical membrane antigen 1 / malaria / RON2 / paramagnetic probe
Function / homologyApical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / membrane => GO:0016020 / Alpha Beta / Apical membrane antigen-1
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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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: RON2 peptide


Theoretical massNumber of molelcules
Total (without water)39,9412
Polymers39,9412
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-10 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.565, 37.975, 72.016
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apical membrane antigen-1


Mass: 38391.840 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) / References: UniProt: Q1PBJ5
#2: Protein/peptide RON2 peptide


Mass: 1548.870 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 41.36 %
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: 2.1→36.273 Å / Num. obs: 19742 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 5.75
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 5980

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1A

4r1a


Resolution: 2.1→36.273 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 995 5.04 %
Rwork0.2069 --
obs0.2088 19733 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 0 164 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032249
X-RAY DIFFRACTIONf_angle_d0.6233051
X-RAY DIFFRACTIONf_dihedral_angle_d10.464807
X-RAY DIFFRACTIONf_chiral_restr0.024324
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21070.30211280.2652672X-RAY DIFFRACTION100
2.2107-2.34920.30991140.24732654X-RAY DIFFRACTION100
2.3492-2.53060.28011410.23762663X-RAY DIFFRACTION100
2.5306-2.78510.25371710.23312636X-RAY DIFFRACTION100
2.7851-3.1880.23931250.21522680X-RAY DIFFRACTION100
3.188-4.01570.21681700.17622660X-RAY DIFFRACTION100
4.0157-36.27860.21611460.17422773X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 144.5045 Å / Origin y: -6.4144 Å / Origin z: 92.8503 Å
111213212223313233
T0.1353 Å20.0235 Å2-0.022 Å2-0.1203 Å2-0.0067 Å2--0.161 Å2
L0.6581 °20.3408 °2-0.5095 °2-0.6228 °2-0.3076 °2--2.5635 °2
S-0.006 Å °-0.0303 Å °0.043 Å °-0.0523 Å °0.0157 Å °0.0878 Å °0.0429 Å °-0.2111 Å °-0.0156 Å °
Refinement TLS groupSelection details: all

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