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- PDB-1mma: X-RAY STRUCTURES OF THE MGADP, MGATPGAMMAS, AND MGAMPPNP COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1mma
TitleX-RAY STRUCTURES OF THE MGADP, MGATPGAMMAS, AND MGAMPPNP COMPLEXES OF THE DICTYOSTELIUM DISCOIDEUM MYOSIN MOTOR DOMAIN
ComponentsMYOSIN
KeywordsCOILED COIL / MYOSIN / DICTYOSTELIUM / MOTOR / NUCLEOTIDE ANALOGUES / ADP / ATPASE / ACTIN-BINDING
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 / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization ...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 / pseudopodium retraction / 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 / calcium-dependent ATPase activity / hypotonic response / actomyosin contractile ring / uropod / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / substrate-dependent cell migration, cell extension / bleb assembly / actomyosin / filopodium assembly / myosin filament / early phagosome / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to cAMP / response to mechanical stimulus / 14-3-3 protein binding / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cytoplasmic vesicle / cell cortex / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGulick, A.M. / Bauer, C.B. / Thoden, J.B. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1997
Title: X-ray structures of the MgADP, MgATPgammaS, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain.
Authors: Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Rayment, I.
#1: Journal: Biochemistry / Year: 1995
Title: X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp(Dot)Befx and Mgadp(Dot)Alf4-
Authors: Fisher, A.J. / Smith, C.A. / Thoden, J.B. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I.
History
DepositionJul 18, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2723
Polymers86,8201
Non-polymers4522
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.600, 179.000, 53.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MYOSIN


Mass: 86820.219 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: Q760L, R761P, I762N
Source method: isolated from a genetically manipulated source
Details: GENETICALLY TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM. LIGANDS MG2+, ADP
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799, EC: 3.6.1.32
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.3 %PEG800011
250 mMHEPES11
3125 mM11NaCl
43 mMdithiothreitol11
51.2 mM11MgCl2
61.2 mMnucleotide11
75 mg/mlprotein11

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorDate: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 56984 / % possible obs: 96.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.6
Reflection shellResolution: 2.1→2.19 Å / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 189699
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MMD

1mmd


Resolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.219 --
obs-56984 96.2 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 28 424 6139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.5
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.3 Å2
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.009

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