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- PDB-2mys: MYOSIN SUBFRAGMENT-1, ALPHA CARBON COORDINATES ONLY FOR THE TWO L... -

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Basic information

Entry
Database: PDB / ID: 2mys
TitleMYOSIN SUBFRAGMENT-1, ALPHA CARBON COORDINATES ONLY FOR THE TWO LIGHT CHAINS
Components(MYOSIN) x 3
KeywordsMUSCLE PROTEIN / MYOSIN SUBFRAGMENT-1 / MYOSIN HEAD / MOTOR PROTEIN
Function / homology
Function and homology information


regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin complex / myosin II complex / microfilament motor activity / myofibril / skeletal muscle tissue development / muscle contraction ...regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin complex / myosin II complex / microfilament motor activity / myofibril / skeletal muscle tissue development / muscle contraction / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / 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 / EF-hand domain / Kinesin motor domain / Kinesin / DNA repair protein XRCC4-like, C-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / 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 / EF-hand domain / Kinesin motor domain / Kinesin / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / EF-hand, calcium binding motif / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
Myosin light chain 1, skeletal muscle isoform / Myosin light chain 3, skeletal muscle isoform / Myosin regulatory light chain 11 / Myosin heavy chain, skeletal muscle, adult
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRayment, I. / Holden, H.M.
Citation
Journal: Science / Year: 1993
Title: Three-dimensional structure of myosin subfragment-1: a molecular motor.
Authors: Rayment, I. / Rypniewski, W.R. / Schmidt-Base, K. / Smith, R. / Tomchick, D.R. / Benning, M.M. / Winkelmann, D.A. / Wesenberg, G. / Holden, H.M.
#1: Journal: Biochemistry / Year: 1995
Title: X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp.Befx and Mgadp.Alf4-
Authors: Fisher, A.J. / Smith, C.A. / Thoden, J.B. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I.
#2: Journal: Biochemistry / Year: 1995
Title: X-Ray Structure of the Magnesium(II)-Pyrophosphate Complex of the Truncated Head of Dictyostelium Discoideum Myosin to 2.7 A Resolution
Authors: Smith, C.A. / Rayment, I.
History
DepositionJun 27, 1996Processing site: BNL
SupersessionJan 11, 1997ID: 1MYS
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN
B: MYOSIN
C: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6715
Polymers131,5513
Non-polymers1202
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.400, 124.200, 274.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MYOSIN


Mass: 96880.750 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT-1 / Source method: isolated from a natural source
Details: PROTEOLYTIC FRAGMENT OF MYOSIN GENERATED BY PAPAIN DIGESTION
Source: (natural) Gallus gallus (chicken) / Organ: SKELETAL / Tissue: PECTORALIS MUSCLE / References: UniProt: P13538
#2: Protein MYOSIN / Coordinate model: Cα atoms only


Mass: 18329.598 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT-1 / Source method: isolated from a natural source
Details: PROTEOLYTIC FRAGMENT OF MYOSIN GENERATED BY PAPAIN DIGESTION
Source: (natural) Gallus gallus (chicken) / Organ: SKELETAL / Tissue: PECTORALIS MUSCLE / References: UniProt: P02609
#3: Protein MYOSIN / Coordinate model: Cα atoms only


Mass: 16340.213 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT-1 / Source method: isolated from a natural source
Details: PROTEOLYTIC FRAGMENT OF MYOSIN GENERATED BY PAPAIN DIGESTION
Source: (natural) Gallus gallus (chicken) / Organ: SKELETAL / Tissue: PECTORALIS MUSCLE / References: UniProt: P02605, UniProt: P02604*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal grow
*PLUS
pH: 6.7 / Method: batch method / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.35 Mammonium salfate11
2500 mMpotassium chloride11
350 mMpotassium phosphate11
45 mMdithiothreitol12
50.5 mM12
68-12 mg/mlprtein12

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 4.5 Å / Num. obs: 36781 / Num. measured all: 178986 / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
TNTrefinement
XDSdata reduction
ROSSMANNSOFTWAREdata reduction
CCP4data scaling
RefinementResolution: 2.8→30 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.223 -
obs-36781
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 6 0 6788
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.5

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