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- PDB-4z09: Crystal structure of FVO strain Plasmodium falciparum AMA1 in com... -

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Basic information

Entry
Database: PDB / ID: 4z09
TitleCrystal structure of FVO strain Plasmodium falciparum AMA1 in complex with the RON2hp [Thr2040Ala] peptide
Components
  • Apical membrane antigen 1
  • Rhoptry neck protein 2
KeywordsCELL INVASION / inhibitor / AMA1 / malaria
Function / homology
Function and homology information


rhoptry neck / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / 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
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum Vietnam Oak-Knoll (eukaryote)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, G. / McGowan, S. / Norton, R.S. / Scanlon, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1025150 Australia
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure-Activity Studies of beta-Hairpin Peptide Inhibitors of the Plasmodium falciparum AMA1-RON2 Interaction.
Authors: Wang, G. / Drinkwater, N. / Drew, D.R. / MacRaild, C.A. / Chalmers, D.K. / Mohanty, B. / Lim, S.S. / Anders, R.F. / Beeson, J.G. / Thompson, P.E. / McGowan, S. / Simpson, J.S. / Norton, R.S. / Scanlon, M.J.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1
C: Rhoptry neck protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9093
Polymers39,8172
Non-polymers921
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.075, 72.025, 115.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apical membrane antigen 1 /


Mass: 38333.805 Da / Num. of mol.: 1 / Fragment: UNP residues 104-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote)
Strain: FVO / Gene: PFFVO_05649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A024UZE1
#2: Protein/peptide Rhoptry neck protein 2


Mass: 1482.769 Da / Num. of mol.: 1 / Fragment: UNP residues 1217-1229 / Mutation: T2040A / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IKV6*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 15-20% PEG400, 0.1 M Tris-HCl, pH 8.6, 0.1 M sodium acetate and 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9464 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 2→38.07 Å / Num. obs: 21689 / % possible obs: 97.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.071 / Net I/σ(I): 10.8 / Num. measured all: 227394 / Scaling rejects: 377
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.057.70.85241114814390.5240.32691.5
8.94-38.0710.10.12318.931193090.8170.04399.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.2.17data scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1A

4r1a


Resolution: 2→36.157 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 1061 4.9 %
Rwork0.1957 20574 -
obs0.1974 21635 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 20.882 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: final / Resolution: 2→36.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 6 176 2393
Biso mean--42.76 24.36 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022289
X-RAY DIFFRACTIONf_angle_d0.5753101
X-RAY DIFFRACTIONf_chiral_restr0.023329
X-RAY DIFFRACTIONf_plane_restr0.002408
X-RAY DIFFRACTIONf_dihedral_angle_d11.424821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.09130.25971210.23472366248792
2.0913-2.20160.27061420.21332387252993
2.2016-2.33950.22271300.2082539266998
2.3395-2.52010.23871450.20172576272199
2.5201-2.77360.24841200.21392585270599
2.7736-3.17480.22641360.202126412777100
3.1748-3.9990.22151190.168326792798100
3.999-36.16330.20521480.183528012949100
Refinement TLS params.Method: refined / Origin x: -8.7489 Å / Origin y: 2.6222 Å / Origin z: -6.9913 Å
111213212223313233
T0.0943 Å2-0.001 Å20.0356 Å2-0.085 Å2-0.0026 Å2--0.0853 Å2
L0.9334 °2-0.2817 °20.3453 °2-2.3581 °2-0.433 °2--0.5989 °2
S0.0186 Å °0.1001 Å °0.056 Å °-0.2091 Å °-0.008 Å °-0.0077 Å °-0.0138 Å °0.0254 Å °-0.0157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA108 - 438
2X-RAY DIFFRACTION1allC1 - 13
3X-RAY DIFFRACTION1allS1 - 293
4X-RAY DIFFRACTION1allB1

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