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- PDB-1dfl: SCALLOP MYOSIN S1 COMPLEXED WITH MGADP:VANADATE-TRANSITION STATE -

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Basic information

Entry
Database: PDB / ID: 1dfl
TitleSCALLOP MYOSIN S1 COMPLEXED WITH MGADP:VANADATE-TRANSITION STATE
Components(MYOSIN HEAD) x 3
KeywordsCONTRACTILE PROTEIN / MYOSIN MOTOR / CONFORMATIONAL CHANGES
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
: / 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. ...: / 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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / 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 / Resolution: 4.2 Å
AuthorsHoudusse, A. / Szent-Gyorgyi, A.G. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Three conformational states of scallop myosin S1.
Authors: Houdusse, A. / 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.
#2: Journal: Structure / Year: 1996
Title: Structure of the Regulatory Domain of Scallop Myosin at 2 A Resolution: Implications for Regulation.
Authors: Houdusse, A. / Cohen, C.
History
DepositionNov 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_asym_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.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_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 HEAD
Y: MYOSIN HEAD
Z: MYOSIN HEAD
B: MYOSIN HEAD
W: MYOSIN HEAD
X: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,10816
Polymers255,8466
Non-polymers1,26210
Water00
1
A: MYOSIN HEAD
Y: MYOSIN HEAD
Z: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polymers127,9233
Non-polymers6315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOSIN HEAD
W: MYOSIN HEAD
X: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polymers127,9233
Non-polymers6315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.032, 243.475, 124.650
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ABYWZX

#1: Protein MYOSIN HEAD


Mass: 94843.883 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P24733
#2: Protein MYOSIN HEAD


Mass: 15914.102 Da / Num. of mol.: 2 / Fragment: REGULATORY LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P13543
#3: Protein MYOSIN HEAD


Mass: 17165.070 Da / Num. of mol.: 2 / Fragment: ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P07291

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Non-polymers , 4 types, 10 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMcacodylate1reservoir
350 mMammonium sulfate1reservoir
410 mM1reservoirMgCl2
515 %(v/v)glycerol1reservoir
67 %(v/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. obs: 426824 / % possible obs: 95.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.4
Reflection shellResolution: 3.8→3.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.216 / % possible all: 80.9
Reflection
*PLUS
Highest resolution: 3.8 Å / Lowest resolution: 40 Å / Num. obs: 29173 / Biso Wilson estimate: 30 Å2 / Num. measured all: 426824
Reflection shell
*PLUS
% possible obs: 80.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 4.2→20 Å / σ(F): 1
Details: AT THIS RESOLUTION, WE PERFORMED ONLY A RIGID BODY REFINEMENT. NO POSITIONAL REFINEMENT WAS DONE.
RfactorNum. reflection% reflection
Rfree0.4 1128 -
Rwork0.394 --
obs0.394 22179 95 %
Refinement stepCycle: LAST / Resolution: 4.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10430 0 70 0 10500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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