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- PDB-1d0y: DICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1d0y
TitleDICTYOSTELIUM MYOSIN S1DC (MOTOR DOMAIN FRAGMENT) COMPLEXED WITH O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM FLUORIDE.
ComponentsMYOSIN S1DC MOTOR DOMAIN
KeywordsCONTRACTILE PROTEIN / MYOSIN / MOTILITY / ACTIN-BINDING / MOTOR DOMAIN / NANOLOGS
Function / homology
Function and homology information


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 / RHO GTPases activate PAKs / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge ...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 / RHO GTPases activate PAKs / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / calcium-dependent ATPase activity / actomyosin contractile ring / hypotonic response / uropod / filopodium assembly / negative regulation of actin filament polymerization / apical cortex / bleb assembly / actin-myosin filament sliding / detection of mechanical stimulus / substrate-dependent cell migration, cell extension / actomyosin / early phagosome / myosin filament / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / cleavage furrow / pseudopodium / mitotic cytokinesis / cytoskeletal motor activity / response to cAMP / response to mechanical stimulus / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / chemotaxis / intracellular protein localization / regulation of cell shape / actin filament binding / cytoplasmic vesicle / extracellular matrix / cell cortex / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal ...Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ONP / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGulick, A.M. / Bauer, C.B. / Thoden, J.B. / Pate, E. / Yount, R.G. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs.
Authors: Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Pate, E. / Yount, R.G. / Rayment, I.
History
DepositionSep 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN S1DC MOTOR DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1673
Polymers86,7351
Non-polymers4312
Water12,755708
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.8, 180.3, 54.0
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MYOSIN S1DC MOTOR DOMAIN


Mass: 86735.109 Da / Num. of mol.: 1 / Fragment: S1DC MOTOR DOMAIN / Mutation: Q760P, R761N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ONP / O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE


Mass: 407.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11BeF3N2O9P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7
Details: 8.3 % PEG 8000 125 MM NACL 3 MM DTT, pH 7.0, MICROBATCH, temperature 4.0K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
28.3 %PEG800011
350 mMHEPES11
4125 mM11NaCl
53 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jun 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 59396 / Num. obs: 59396 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.45 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 0.148 / % possible all: 78.2
Reflection
*PLUS
Num. all: 68586 / Num. measured all: 146074
Reflection shell
*PLUS
% possible obs: 78.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rwork0.178 --
all0.178 59396 -
obs0.178 59396 86.6 %
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 26 708 6623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.57
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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