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- PDB-1scm: STRUCTURE OF THE REGULATORY DOMAIN OF SCALLOP MYOSIN AT 2.8 ANGST... -

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Basic information

Entry
Database: PDB / ID: 1scm
TitleSTRUCTURE OF THE REGULATORY DOMAIN OF SCALLOP MYOSIN AT 2.8 ANGSTROMS RESOLUTION
Components
  • MYOSIN ESSENTIAL LIGHT CHAIN
  • MYOSIN HEAVY CHAINMyosin
  • MYOSIN REGULATORY LIGHT CHAIN
KeywordsCALCIUM-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 / SYNCHROTRON / Resolution: 2.8 Å
AuthorsCohen, C. / Xie, X.
Citation
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.
#1: 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 6, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Feb 14, 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_atom_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_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_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

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)40,8715
Polymers40,7913
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-73 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 87.000, 55.500
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: LEU B 12 - PRO B 13 OMEGA =217.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein MYOSIN HEAVY CHAIN / Myosin


Mass: 7483.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians (bay scallop) / References: UniProt: P24733
#2: Protein MYOSIN REGULATORY LIGHT CHAIN


Mass: 16516.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians (bay scallop) / References: UniProt: P13543
#3: Protein MYOSIN ESSENTIAL LIGHT CHAIN


Mass: 16791.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians (bay scallop) / References: UniProt: P07291
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MLR_AEQIR SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 86 GLU 86 ASN 101 THR 101 TWO ERRORS WERE FOUND IN THE ORIGINAL RLC SEQUENCE BY DRS. GOODWIN, LEINWAND AND SZENT-GYORGYI (J.MOL.BIOL. 216, 85-93 TO BE CORRECT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
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

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 10352 / % possible obs: 91 % / Observed criterion σ(I): 1 / Num. measured all: 30711 / Rmerge(I) obs: 0.113

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→10 Å
Details: THE ELECTRON DENSITY FOR LEU (B12) AND PRO (B13) WHICH ARE THE FIRST TWO RESIDUES IN THE RLC IS NOT CLEAR ENOUGH TO DEFINE THE GEOMETRY WELL.
RfactorNum. reflection
Rwork0.201 -
obs0.201 8960
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 2 0 2816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 8960 / σ(F): 2 / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.76

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