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- PDB-6tj7: T. gondii myosin A trimeric complex -

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Basic information

Entry
Database: PDB / ID: 6tj7
TitleT. gondii myosin A trimeric complex
Components
  • Calmodulin, putative
  • Myosin light chain TgMLC1
  • Myosin-A
KeywordsMOTOR PROTEIN / motility / glideosome / light chain / myosin
Function / homology
Function and homology information


myosin II complex / myosin complex / microfilament motor activity / actin filament organization / actin filament binding / calcium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / : / EF-hand domain / EF hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / : / EF-hand domain / EF hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / : / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
HEXANE-1,6-DIOL / 1,3-PROPANDIOL / Calmodulin, putative / Myosin-A / Calmodulin
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPazicky, S. / Loew, C.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
Other private800026 Germany
Swedish Research Council621-2013-5905 Sweden
CitationJournal: Commun Biol / Year: 2020
Title: Structural role of essential light chains in the apicomplexan glideosome.
Authors: Pazicky, S. / Dhamotharan, K. / Kaszuba, K. / Mertens, H.D.T. / Gilberger, T. / Svergun, D. / Kosinski, J. / Weininger, U. / Low, C.
History
DepositionNov 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Calmodulin, putative
B: Myosin light chain TgMLC1
C: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2399
Polymers37,6993
Non-polymers5406
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS data confirmed the presence of hetero-trimeric complex in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-49 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.630, 93.482, 108.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Calmodulin, putative / Putative calmodulin


Mass: 15490.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_305050 / Plasmid: pET28a(+)-TEV / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B9PZ33
#2: Protein Myosin light chain TgMLC1


Mass: 17198.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pNIC_CTHF / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q95UJ7

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Myosin-A / MyoA / TgM-A


Mass: 5009.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) / References: UniProt: O00934

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Non-polymers , 6 types, 82 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: imidazole, MES monohydrate, PEG 500 MME, PEG 20000, 1-6-hexadiol, 1-butanol, 1,2-propanediol, 2-propnaol, 1,4-butandiol, 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.032 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.032 Å / Relative weight: 1
ReflectionResolution: 2.3→46.74 Å / Num. obs: 19409 / % possible obs: 99.84 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Rrim(I) all: 0.08 / Net I/σ(I): 13.83
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 12474 / CC1/2: 0.58 / Rpim(I) all: 0.43 / Rrim(I) all: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tgh

3tgh


Resolution: 2.3→40.96 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4769
RfactorNum. reflection% reflection
Rfree0.2189 952 4.91 %
Rwork0.1864 --
obs0.1881 19406 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 33 76 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712655
X-RAY DIFFRACTIONf_angle_d0.87183564
X-RAY DIFFRACTIONf_chiral_restr0.049378
X-RAY DIFFRACTIONf_plane_restr0.0053469
X-RAY DIFFRACTIONf_dihedral_angle_d12.5344365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.29781400.24232558X-RAY DIFFRACTION99.05
2.42-2.570.2891330.24792597X-RAY DIFFRACTION99.93
2.57-2.770.29861350.24512627X-RAY DIFFRACTION99.89
2.77-3.050.28491300.22162615X-RAY DIFFRACTION100
3.05-3.490.26891380.20242628X-RAY DIFFRACTION100
3.49-4.40.18331450.16612653X-RAY DIFFRACTION99.96
4.4-40.960.16471310.15492776X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 57.0852869024 Å / Origin y: 31.6228176444 Å / Origin z: 41.8751877451 Å
111213212223313233
T0.313195647475 Å20.0515472926394 Å20.0262994596981 Å2-0.460622912137 Å20.0762863801032 Å2--0.282558884274 Å2
L1.34515455896 °21.4652030306 °20.0495375441358 °2-3.20945280214 °2-0.729802265625 °2--1.18900640943 °2
S0.0276698247798 Å °-0.302264490384 Å °-0.196173717895 Å °0.0022194761302 Å °-0.255393782514 Å °-0.170180202122 Å °-0.0919813428593 Å °0.0371344800954 Å °0.227364426209 Å °
Refinement TLS groupSelection details: all

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