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- PDB-3sri: Crystal structure of Plasmodium falciparum AMA1 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3sri
TitleCrystal structure of Plasmodium falciparum AMA1 in complex with a 29aa PfRON2 peptide
Components
  • Apical membrane antigen 1
  • Rhoptry neck protein 2
KeywordsCELL INVASION / AMA1 / Plasmodium falciparum / RON2 / 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 (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVulliez-Le Normand, B. / Saul, F.A. / Bentley, G.A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural and functional insights into the malaria parasite moving junction complex.
Authors: Vulliez-Le Normand, B. / Tonkin, M.L. / Lamarque, M.H. / Langer, S. / Hoos, S. / Roques, M. / Saul, F.A. / Faber, B.W. / Bentley, G.A. / Boulanger, M.J. / Lebrun, M.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1
B: Rhoptry neck protein 2


Theoretical massNumber of molelcules
Total (without water)46,7012
Polymers46,7012
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-15 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.724, 38.137, 72.078
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43664.867 Da / Num. of mol.: 1 / Fragment: AMA1 / Mutation: N162K, T288V, S373D, N422D, S423K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: CAMP/Malaysia / Gene: AMA-1, PF83 / Production host: Pichia pastoris (fungus) / References: UniProt: P50489
#2: Protein/peptide Rhoptry neck protein 2


Mass: 3036.505 Da / Num. of mol.: 1 / Fragment: RON2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IKV6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 20% PEG 4000, 0.1M Tris/HCL, 0.1M sodium acetate, 20% isopropanol, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95367 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95367 Å / Relative weight: 1
ReflectionResolution: 1.6→46.97 Å / Num. all: 48207 / Num. obs: 48207 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 22.19 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6821 / % possible all: 92.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z40

1z40


Resolution: 1.6→35.04 Å / Cor.coef. Fo:Fc: 0.9517 / Cor.coef. Fo:Fc free: 0.9475 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 2462 5.11 %RANDOM
Rwork0.1763 ---
all0.1772 48205 --
obs0.1772 48205 94.9 %-
Displacement parametersBiso mean: 29.98 Å2
Baniso -1Baniso -2Baniso -3
1--4.9819 Å20 Å2-0.9063 Å2
2---0.6906 Å20 Å2
3---5.6725 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 0 265 2725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONo_bond_d0.012571HARMONIC2
X-RAY DIFFRACTIONo_angle_deg1.043493HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion19.45
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2469 147 4.22 %
Rwork0.2296 3337 -
all0.2304 3484 -
obs-3834 94.9 %

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