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- PDB-1w9i: Myosin II Dictyostelium discoideum motor domain S456Y bound with ... -

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Basic information

Entry
Database: PDB / ID: 1w9i
TitleMyosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-BeFx
ComponentsMYOSIN II HEAVY CHAIN
KeywordsMYOSIN / MOLECULAR MOTOR / ATPASE / 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 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / 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 / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / muscle contraction / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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. ...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. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.1Dec 28, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 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 / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)89,33019
Polymers87,8811
Non-polymers1,44918
Water13,223734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.017, 186.506, 54.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 87881.344 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-754 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MGADP-BEFX / 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, 752 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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE ASP 2 ASN, CHAIN A ENGINEERED RESIDUE SER 456 TYR, CHAIN A MYOSIN IS A PROTEIN ...ENGINEERED RESIDUE ASP 2 ASN, CHAIN A ENGINEERED RESIDUE SER 456 TYR, CHAIN A MYOSIN IS A PROTEIN THAT BINDS TO ACTIN AND HAS ATPASE ACTIVITY THAT IS ACTIVATED BY ACTIN.

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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: 3.2 Å3/Da / Density % sol: 60.8 %
Crystal growpH: 7
Details: 10% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE RESERVOIR AND 7% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9767
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 105022 / % possible obs: 96.1 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.1 / % possible all: 97.4

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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 1MMA

1mma


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.639 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5227 5 %RANDOM
Rwork0.182 ---
obs0.183 99718 96.1 %-
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: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5551 0 92 734 6377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215850
X-RAY DIFFRACTIONr_bond_other_d0.0020.025228
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9567882
X-RAY DIFFRACTIONr_angle_other_deg0.803312200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345698
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_restr0.0970.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021172
X-RAY DIFFRACTIONr_nbd_refined0.1930.2961
X-RAY DIFFRACTIONr_nbd_other0.220.25292
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.22848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2425
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6691.53517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27925696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59432333
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7584.52186
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.21 377
Rwork0.186 7371

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