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- PDB-4r1a: Crystal Structure of FVO strain Plasmodium falciparum AMA1 -

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Basic information

Entry
Database: PDB / ID: 4r1a
TitleCrystal Structure of FVO strain Plasmodium falciparum AMA1
ComponentsApical membrane antigen 1
KeywordsCELL INVASION / PAN fold / erythrocyte invasion by merozoites / RON2 / Moving junction complex
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesPlasmodium falciparum FCR-3/Gambia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLim, S.S. / Norton, R.S. / McGowan, S.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO.
Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P. ...Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P.J. / Norton, R.S. / McGowan, S.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
Revision 1.2Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)38,3341
Polymers38,3341
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.794, 37.788, 71.706
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


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 FCR-3/Gambia (eukaryote)
Strain: isolate FCR-3 / Gambia / Gene: AMA-1, PF83 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P50490
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25.0% (v/v) PEG 3350, 0.1 M HEPES, 0.2 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→35.72 Å / Num. obs: 19576 / % possible obs: 97.5 % / Observed criterion σ(I): 8 / Biso Wilson estimate: 21.8 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z40

1z40


Resolution: 2→35.72 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 1004 5.14 %5%
Rwork0.1993 ---
obs0.2026 19576 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 135 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072093
X-RAY DIFFRACTIONf_angle_d0.9792838
X-RAY DIFFRACTIONf_dihedral_angle_d12.243734
X-RAY DIFFRACTIONf_chiral_restr0.038303
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10550.40051310.30912604X-RAY DIFFRACTION96
2.1055-2.23740.31241380.25992622X-RAY DIFFRACTION96
2.2374-2.41010.31661260.2242615X-RAY DIFFRACTION97
2.4101-2.65260.27711340.21572657X-RAY DIFFRACTION97
2.6526-3.03630.29771630.19632613X-RAY DIFFRACTION97
3.0363-3.82470.20061490.16322650X-RAY DIFFRACTION97
3.8247-35.720.23481630.17192759X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -22.3982 Å / Origin y: 2.2987 Å / Origin z: 16.6863 Å
111213212223313233
T0.4537 Å2-0.0268 Å20.0593 Å2-0.0995 Å20.002 Å2--0.1132 Å2
L0.7601 °2-0.478 °2-0.4025 °2-1.2354 °20.4462 °2--2.6744 °2
S-0.0362 Å °0.0262 Å °0.0038 Å °-0.0768 Å °0.0684 Å °-0.0935 Å °0.1451 Å °0.2295 Å °-0.0342 Å °
Refinement TLS groupSelection details: all

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