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- PDB-8exw: Drosophila melanogaster indirect flight muscle myosin II (subfrag... -

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Basic information

Entry
Database: PDB / ID: 8exw
TitleDrosophila melanogaster indirect flight muscle myosin II (subfragment-1)
Components
  • Isoform K of Myosin heavy chain, muscle
  • Myosin light chain alkali
KeywordsMOTOR PROTEIN / Insect Muscle Myosin Powers Flight / Drosophila melanogaster / skeletal muscle myosin II / indirect flight muscle isoform / subfragment-1 / Dmel / IFI
Function / homology
Function and homology information


myosin filament organization / flight / adult somatic muscle development / muscle thin filament assembly / regulation of myosin II filament assembly / polytene chromosome puff / epithelial cell migration, open tracheal system / border follicle cell migration / striated muscle myosin thick filament / myofibril assembly ...myosin filament organization / flight / adult somatic muscle development / muscle thin filament assembly / regulation of myosin II filament assembly / polytene chromosome puff / epithelial cell migration, open tracheal system / border follicle cell migration / striated muscle myosin thick filament / myofibril assembly / regulation of catalytic activity / muscle myosin complex / muscle cell differentiation / myosin filament / locomotion / myosin II complex / A band / muscle organ development / structural constituent of muscle / sarcomere organization / microfilament motor activity / myosin heavy chain binding / mesoderm development / enzyme regulator activity / muscle contraction / sarcomere / actin filament binding / calmodulin binding / protein stabilization / calcium ion binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / : / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / : / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Myosin heavy chain, muscle / Myosin light chain alkali
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCaldwell, J.T. / Huxford, T. / Bernstein, S.I. / Stec, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM032443 United States
CitationJournal: To Be Published
Title: Drosophila melanogaster indirect flight muscle myosin II (subfragment-1)
Authors: Caldwell, J.T. / Huxford, T. / Bernstein, S.I. / Stec, B.
History
DepositionOct 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform K of Myosin heavy chain, muscle
B: Myosin light chain alkali
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5374
Polymers109,0862
Non-polymers4522
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-44 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.394, 126.806, 92.581
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isoform K of Myosin heavy chain, muscle


Mass: 91533.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Tissue: Indirect Flight Muscle / Cell: Muscle / Gene: Mhc, CG17927 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P05661
#2: Protein Myosin light chain alkali


Mass: 17551.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Tissue: Indirect Flight Muscle / Cell: Muscle / Gene: Mlc1, MLC-ALK, CG5596 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06742
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 80% Hampton Research Index screen H11: 0.1 M Potassium thiocyanate, 30 %w/v Polyethylene glycol monomethyl ether 2,000 20% Hampton Research additive screen C3: 0.1 M Phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 31441 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.31 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Χ2: 0.876 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1630 / CC1/2: 0.729 / CC star: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: various

Resolution: 2.5→43.48 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1478 4.7 %
Rwork0.1882 29944 -
obs0.1908 31422 92.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 28 157 7625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037617
X-RAY DIFFRACTIONf_angle_d0.524510257
X-RAY DIFFRACTIONf_chiral_restr0.03691092
X-RAY DIFFRACTIONf_plane_restr0.00321341
X-RAY DIFFRACTIONf_dihedral_angle_d8.97651018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.2757790.21521571X-RAY DIFFRACTION54.35
2.58-2.670.26781180.21412199X-RAY DIFFRACTION74.72
2.67-2.780.29641360.22332696X-RAY DIFFRACTION93.1
2.78-2.90.28291720.22432903X-RAY DIFFRACTION99
2.9-3.060.31551390.21182896X-RAY DIFFRACTION98.86
3.06-3.250.23461430.19552921X-RAY DIFFRACTION98.97
3.25-3.50.23771330.19592905X-RAY DIFFRACTION98.83
3.5-3.850.22261530.18212941X-RAY DIFFRACTION99.61
3.85-4.410.25421350.16592939X-RAY DIFFRACTION100
4.41-5.550.23651240.16652957X-RAY DIFFRACTION99.97
5.55-43.480.20321460.18343016X-RAY DIFFRACTION99.91

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