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- PDB-1w9l: Myosin II Dictyostelium discoideum motor domain S456E bound with ... -

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Basic information

Entry
Database: PDB / ID: 1w9l
TitleMyosin II Dictyostelium discoideum motor domain S456E bound with MgADP-AlF4
ComponentsMYOSIN II HEAVY CHAIN
KeywordsMYOSIN / MOLECULAR MOTOR / POWERSTROKE / MOTOR DOMAIN / MUTANT / MUSCLE CONTRACTION
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / hypotonic response / actomyosin contractile ring / uropod / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / filopodium assembly / myosin filament / early phagosome / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / 14-3-3 protein binding / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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) ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMorris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L.
CitationJournal: To be Published
Title: Structure-Function Analysis of Myosin II Backdoor Mutants
Authors: Morris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L.
History
DepositionOct 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN II HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,79010
Polymers87,8631
Non-polymers9279
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.038, 145.983, 152.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MYOSIN II HEAVY CHAIN / NON MUSCLE / MYOSIN II DICTYOSTELIUM DISCOIDEUM


Mass: 87863.281 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-759 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MGADP-ALF4 / Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P08799, EC: 3.6.4.1

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Non-polymers , 5 types, 444 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE SER 456 GLU, CHAIN A MYOSIN IS A PROTEIN THAT BINDS TO ACTIN AND HAS ATPASE ...ENGINEERED RESIDUE SER 456 GLU, CHAIN A MYOSIN IS A PROTEIN THAT BINDS TO ACTIN AND HAS ATPASE ACTIVITY THAT IS ACTIVATED BY ACTIN.
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: 2.9 Å3/Da / Density % sol: 57.1 %
Crystal growpH: 7
Details: 12% PEG 8000, 50 MM HEPES PH 7, 100 MM NACL, 2 MM DTT, 2 MM NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 71088 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MND

1mnd


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.448 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3525 5 %RANDOM
Rwork0.193 ---
obs0.194 66558 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--2.97 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 57 435 6216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215902
X-RAY DIFFRACTIONr_bond_other_d0.0020.025214
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9527976
X-RAY DIFFRACTIONr_angle_other_deg0.746312128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026585
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021213
X-RAY DIFFRACTIONr_nbd_refined0.2050.21334
X-RAY DIFFRACTIONr_nbd_other0.240.26392
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2415
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6621.53616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26325806
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88432286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2114.52170
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 258
Rwork0.257 4819

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