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- PDB-1kwo: SCALLOP MYOSIN S1-ATPgammaS-p-PDM IN THE ACTIN-DETACHED CONFORMATION -

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Basic information

Entry
Database: PDB / ID: 1kwo
TitleSCALLOP MYOSIN S1-ATPgammaS-p-PDM IN THE ACTIN-DETACHED CONFORMATION
Components
  • MYOSIN ESSENTIAL LIGHT CHAIN
  • MYOSIN HEAVY CHAIN
  • MYOSIN REGULATORY LIGHT CHAIN
KeywordsCONTRACTILE PROTEIN / Actin-detached / Myosin / Mechanics of Motor / Cross linker
Function / homology
Function and homology information


muscle myosin complex / myosin filament / myosin complex / myosin II complex / microfilament motor activity / myofibril / actin filament binding / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
Myosin S1 fragment, N-terminal / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / 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 S1 fragment, N-terminal / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / 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 / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chem-PDM / Myosin essential light chain, striated adductor muscle / Myosin regulatory light chain, striated adductor muscle / Myosin heavy chain, striated muscle
Similarity search - Component
Biological speciesArgopecten irradians (bay scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsHimmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, G. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystallographic findings on the internally uncoupled and near-rigor states of myosin: Further insights into the mechanics of the motor
Authors: Himmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Atomic Structure of Scallop Myosin Subfragment S1 Complexed with MgADP: A Novel Conformation of the Myosin Head
Authors: Houdusse, A. / Kalabokis, V.N. / Himmel, D. / Szent-Gyorgyi, A.G. / Cohen, C.
History
DepositionJan 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_entry_details ...database_PDB_caveat / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN HEAVY CHAIN
B: MYOSIN REGULATORY LIGHT CHAIN
C: MYOSIN ESSENTIAL LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4188
Polymers130,5143
Non-polymers9045
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-95 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.816, 57.028, 151.708
Angle α, β, γ (deg.)95.16, 96.45, 100.93
Int Tables number1
Space group name H-MP1
DetailsMyosin-S1 consists of three peptide chains (heavy chain, regulatory light chain, essential light chain), which can also be described as a heterotrimer

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein MYOSIN HEAVY CHAIN


Mass: 95317.430 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1) / Source method: isolated from a natural source / Details: PAPAIN DIGESTED / Source: (natural) Argopecten irradians (bay scallop) / Tissue: muscle / References: UniProt: P24733
#2: Protein MYOSIN REGULATORY LIGHT CHAIN / R-LC


Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: muscle / References: UniProt: P13543
#3: Protein MYOSIN ESSENTIAL LIGHT CHAIN / E-LC


Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: muscle / References: UniProt: P07291

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Non-polymers , 5 types, 11 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-PDM / 4-[4-(2,5-DIOXO-PYRROLIDIN-1-YL)-PHENYLAMINO]-4-HYDROXY-BUTYRIC ACID / PARA-PHENYL DIMALEMIDE


Mass: 292.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O5
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 20000, magnesium chloride, ethylene glycol, Tris HCl, ATPgammaS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.087 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 1999
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. all: 14626 / Num. obs: 14451 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 10.6
Reflection shellResolution: 3.8→3.9 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.274 / % possible all: 45.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B7T

1b7t


Resolution: 3.8→36.87 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 294029.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.328 631 4.8 %RANDOM
Rwork0.238 ---
all0.242 13681 --
obs0.238 13050 78.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.1982 Å2 / ksol: 0.203759 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å216.6 Å212.4 Å2
2--21.85 Å211.16 Å2
3----19.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.52 Å
Luzzati d res low-40 Å
Refinement stepCycle: LAST / Resolution: 3.8→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 55 6 8108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d4.41
X-RAY DIFFRACTIONc_mcbond_it9.561.5
X-RAY DIFFRACTIONc_mcangle_it14.542
X-RAY DIFFRACTIONc_scbond_it10.832
X-RAY DIFFRACTIONc_scangle_it15.982.5
LS refinement shellResolution: 3.8→3.91 Å / Rfactor Rfree error: 0.159 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.276 3 2.3 %
Rwork0.256 128 -
obs--9.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4CNS_PP47CNS_PP47
X-RAY DIFFRACTION5CNS_PP47CNS_PP47

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