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- PDB-1dfk: NUCLEOTIDE-FREE SCALLOP MYOSIN S1-NEAR RIGOR STATE -

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Basic information

Entry
Database: PDB / ID: 1dfk
TitleNUCLEOTIDE-FREE SCALLOP MYOSIN S1-NEAR RIGOR 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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

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Assembly

Deposited unit
A: MYOSIN HEAD
Y: MYOSIN HEAD
Z: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8164
Polymers127,7763
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.5, 52.1, 164.6
Angle α, β, γ (deg.)90.00, 100.3, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOSIN HEAD


Mass: 94696.711 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / Fragment: ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P07291
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, ammonium sulfate, cacodylate, glycerol , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
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
27 %(v/v)PEG80001reservoir
350 mMMES1reservoir
43 mM1reservoirMgCl2
50.5 mMMgADP/VO41drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
Detector
IDDetector
1CCD
2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4.2→30 Å / Num. all: 10676 / Num. obs: 139608 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 27
Reflection shellResolution: 4.2→4.27 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.308 / Num. unique all: 461 / % possible all: 85.2
Reflection
*PLUS
Num. obs: 10676 / Num. measured all: 139608
Reflection shell
*PLUS
% possible obs: 85.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 4.2→20 Å / σ(F): 1 / σ(I): 1
Details: At this resolution, we performed only a rigid body refinement. No positional refinement was done.
RfactorNum. reflection% reflection
Rfree0.41 508 -
Rwork0.415 --
all0.415 10676 -
obs0.415 10601 95 %
Refinement stepCycle: LAST / Resolution: 4.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 1 0 5032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.4

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