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- PDB-6due: Toxoplasma gondii MyoA, a Class-XIV myosin, in the pre-powerstrok... -

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Basic information

Entry
Database: PDB / ID: 6due
TitleToxoplasma gondii MyoA, a Class-XIV myosin, in the pre-powerstroke state
ComponentsMyosin A
KeywordsMOTOR PROTEIN / Apicomplexan / Myosin / ATPase
Function / homology
Function and homology information


myosin complex / cytoskeletal motor activity / actin binding / ATP binding / metal ion binding
Similarity search - Function
Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Myosin A
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsPowell, C.J. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)148596 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural and mechanistic insights into the function of the unconventional class XIV myosin MyoA fromToxoplasma gondii.
Authors: Powell, C.J. / Ramaswamy, R. / Kelsen, A. / Hamelin, D.J. / Warshaw, D.M. / Bosch, J. / Burke, J.E. / Ward, G.E. / Boulanger, M.J.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Myosin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1297
Polymers88,2981
Non-polymers8316
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-16 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.250, 96.230, 92.050
Angle α, β, γ (deg.)90.000, 110.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin A


Mass: 88298.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / Gene: TGGT1_235470 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S7W634

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Non-polymers , 5 types, 31 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1:1 protein solution to reservoir solution (22% PEG8000, 200 mM ammonium sulfate, 100 mM MES, pH 6.5), cryoprotectant: reservoir solution + 15% glycerol
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2017
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→85.95 Å / Num. obs: 24306 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.28 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3495 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4BYF

4byf


Resolution: 2.6→48.717 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 31.13
RfactorNum. reflection% reflection
Rfree0.2612 1212 4.99 %
Rwork0.2195 --
obs0.2216 24273 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.27 Å2 / Biso mean: 68.7476 Å2 / Biso min: 28.04 Å2
Refinement stepCycle: final / Resolution: 2.6→48.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 51 25 5900
Biso mean--56.69 53.28 -
Num. residues----737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70410.37311320.33682508264096
2.7041-2.82720.37991320.30472537266997
2.8272-2.97620.30281340.28762532266697
2.9762-3.16260.34841330.26872545267897
3.1626-3.40680.28371330.24792561269497
3.4068-3.74950.26481360.22722567270398
3.7495-4.29180.25631360.19942575271198
4.2918-5.40610.22381360.17352592272898
5.4061-48.72590.20261400.18452644278498
Refinement TLS params.Method: refined / Origin x: 20.9759 Å / Origin y: 2.0842 Å / Origin z: 21.2636 Å
111213212223313233
T0.3873 Å2-0.0068 Å2-0.0355 Å2-0.3486 Å2-0.0488 Å2--0.3781 Å2
L1.7542 °20.3287 °2-0.6435 °2-0.5791 °2-0.1789 °2--1.441 °2
S0.039 Å °-0.0915 Å °0.1363 Å °-0.0639 Å °-0.0141 Å °0.0676 Å °-0.052 Å °-0.2157 Å °-0.0256 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA33 - 777
2X-RAY DIFFRACTION1allA1000 - 1002
3X-RAY DIFFRACTION1allB1 - 3
4X-RAY DIFFRACTION1allS1 - 25

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