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- PDB-1wdc: SCALLOP MYOSIN REGULATORY DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1wdc
TitleSCALLOP MYOSIN REGULATORY DOMAIN
Components(SCALLOP MYOSIN) x 3
KeywordsMUSCLE PROTEIN / MYOSIN / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


myosin filament / myosin complex / myofibril / cytoskeletal motor activity / actin filament binding / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
Myosin, subunit A / Myosin, subunit A / 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. ...Myosin, subunit A / Myosin, subunit A / 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / 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 / Few Secondary Structures / Irregular / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
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 / Resolution: 2 Å
AuthorsHoudusse, A. / Cohen, C.
Citation
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.
#1: Journal: Nature / Year: 1994
Title: Structure of the Regulatory Domain of Scallop Myosin at 2.8 A Resolution
Authors: Xie, X. / Harrison, D.H. / Schlichting, I. / Sweet, R.M. / Kalabokis, V.N. / Szent-Gyorgyi, A.G. / Cohen, C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Isolation of the Regulatory Domain of Scallop Myosin: Role of the Essential Light Chain in Calcium Binding
Authors: Kwon, H. / Goodwin, E.B. / Nyitray, L. / Berliner, E. / O'Neall-Hennessey, E. / Melandri, F.D. / Szent-Gyorgyi, A.G.
History
DepositionJan 19, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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_database_status.process_site / _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: SCALLOP MYOSIN
B: SCALLOP MYOSIN
C: SCALLOP MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2585
Polymers43,1943
Non-polymers642
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-83 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.650, 87.100, 55.500
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein SCALLOP MYOSIN


Mass: 7997.623 Da / Num. of mol.: 1 / Fragment: PROTEOLYTIC FRAGMENT, REGULATORY DOMAIN / Source method: isolated from a natural source / Details: PH 7.0 / Source: (natural) Argopecten irradians (bay scallop) / Organ: SKELETALSkeleton / Tissue: SKELETAL MUSCLE / References: UniProt: P24733
#2: Protein SCALLOP MYOSIN


Mass: 17560.855 Da / Num. of mol.: 1 / Fragment: PROTEOLYTIC FRAGMENT, REGULATORY DOMAIN / Source method: isolated from a natural source / Details: PH 7.0 / Source: (natural) Argopecten irradians (bay scallop) / Organ: SKELETALSkeleton / Tissue: SKELETAL MUSCLE / References: UniProt: P13543
#3: Protein SCALLOP MYOSIN


Mass: 17635.635 Da / Num. of mol.: 1 / Fragment: PROTEOLYTIC FRAGMENT, REGULATORY DOMAIN / Source method: isolated from a natural source / Details: PH 7.0 / Source: (natural) Argopecten irradians (bay scallop) / Organ: SKELETALSkeleton / Tissue: SKELETAL MUSCLE / References: UniProt: P07291

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Non-polymers , 3 types, 166 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE RD FRAGMENT IS A TERNARY COMPLEX OF A PORTION OF HEAVY CHAIN WITH TWO LIGHT CHAINS. CHAIN LABEL ...THE RD FRAGMENT IS A TERNARY COMPLEX OF A PORTION OF HEAVY CHAIN WITH TWO LIGHT CHAINS. CHAIN LABEL A DESIGNATES THE PORTION OF MYOSIN HEAVY CHAIN PRESENT IN THE RD FRAGMENT. CHAIN LABEL B DESIGNATES THE MYOSIN REGULATORY LIGHT CHAIN. CHAIN LABEL C DESIGNATES THE MYOSIN ESSENTIAL LIGHT CHAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 51.9 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Xie, X., (1994) Nature, 368, 306.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mM1dropMgCl2
30.1 mM1dropCaCl2
475 mMHEPES1drop
57-8 %PEG40001drop
614-16 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→100 Å / Num. obs: 26715 / % possible obs: 89.2 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. obs: 26725 / Num. measured all: 104023

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 2
Details: SIDE CHAIN ATOMS OF RESIDUE GLU B 153 ARE NOT SEEN IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.281 2665 -
Rwork0.194 --
obs0.194 23375 85.86 %
Displacement parametersBiso mean: 36.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 2 164 3065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.439
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.13
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.428
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 24.135

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