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- PDB-4r1b: Crystal Structure of 3D7 strain Plasmodium falciparum AMA1 -

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Basic information

Entry
Database: PDB / ID: 4r1b
TitleCrystal Structure of 3D7 strain Plasmodium falciparum AMA1
ComponentsApical membrane antigen 1, AMA1
KeywordsCELL INVASION / PAN fold / erythrocyte invasion by merozoites / RON2 / Moving junction complex
Function / homology
Function and homology information


apical complex / microneme / host cell surface binding / symbiont entry into host / 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
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 ...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_struct_special_symmetry
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, AMA1


Theoretical massNumber of molelcules
Total (without water)38,3601
Polymers38,3601
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.920, 51.416, 87.567
Angle α, β, γ (deg.)90.00, 114.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Protein Apical membrane antigen 1, AMA1


Mass: 38360.047 Da / Num. of mol.: 1 / Fragment: UNP residues 104-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: AMA1, PF11_0344 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q7KQK5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12-15% (v/v) polyethylene glycol 3350, 0.02 M MES and 10 mM manganese chloride. Crystals were dehydrated overnight in reservoir solution with increased (35%) (v/v) polyethylene glycol 3350 ...Details: 12-15% (v/v) polyethylene glycol 3350, 0.02 M MES and 10 mM manganese chloride. Crystals were dehydrated overnight in reservoir solution with increased (35%) (v/v) polyethylene glycol 3350 before cryo-stabilisation in 38% (v/v) polyethylene glycol 3350, 0.088 M MES (pH 6.0) and 44 mM manganese chloride for 6-8 h prior to data collection. MilliQ water was added to the stabilisation solution, 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: Nov 30, 2013
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: 1.6→41.07 Å / Num. obs: 40241 / % possible obs: 100 % / Observed criterion σ(I): 8

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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 ID: 1Z40

1z40


Resolution: 1.6→37.454 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 2016 5.01 %5%
Rwork0.182 ---
obs0.1833 40228 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 0 296 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062244
X-RAY DIFFRACTIONf_angle_d0.9863043
X-RAY DIFFRACTIONf_dihedral_angle_d12.503797
X-RAY DIFFRACTIONf_chiral_restr0.042331
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28131420.29212715X-RAY DIFFRACTION100
1.64-1.68440.29171620.27412726X-RAY DIFFRACTION100
1.6844-1.73390.29511140.25182696X-RAY DIFFRACTION100
1.7339-1.78990.22711540.22452706X-RAY DIFFRACTION100
1.7899-1.85390.26671460.21082710X-RAY DIFFRACTION100
1.8539-1.92810.23591370.21042716X-RAY DIFFRACTION100
1.9281-2.01580.21661570.17852706X-RAY DIFFRACTION100
2.0158-2.12210.20391530.16982706X-RAY DIFFRACTION100
2.1221-2.2550.17711670.16422724X-RAY DIFFRACTION100
2.255-2.42910.19691430.16562710X-RAY DIFFRACTION100
2.4291-2.67350.21371350.17432775X-RAY DIFFRACTION100
2.6735-3.06020.21571380.17342730X-RAY DIFFRACTION100
3.0602-3.85490.19281310.15752763X-RAY DIFFRACTION100
3.8549-37.4540.17061370.1652829X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.3118 Å / Origin y: 11.5211 Å / Origin z: 104.7439 Å
111213212223313233
T0.2142 Å2-0.0007 Å20.0647 Å2-0.0986 Å2-0.0016 Å2--0.0985 Å2
L1.8294 °20.2393 °2-0.2561 °2-3.0142 °20.0406 °2--1.7969 °2
S0.0193 Å °0.2427 Å °0.0284 Å °-0.6846 Å °0.0157 Å °-0.2869 Å °-0.0883 Å °0.067 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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