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- PDB-3jtd: Calcium-free Scallop Myosin Regulatory Domain with ELC-D19A Point... -

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Basic information

Entry
Database: PDB / ID: 3jtd
TitleCalcium-free Scallop Myosin Regulatory Domain with ELC-D19A Point Mutation
Components
  • Myosin essential light chain, striated adductor muscle
  • Myosin heavy chain, striated adductor muscleMyosin
  • Myosin regulatory light chain, striated adductor muscle
KeywordsCONTRACTILE PROTEIN / Regulated myosins / smooth and molluscan muscle / X-ray crystallographic structure / scallop regulatory domain/lever arm / off-state / Actin-binding / ATP-binding / Calmodulin-binding / Coiled coil / Cytoplasm / Motor protein / Muscle protein / Myosin / Nucleotide-binding / Thick filament / Calcium
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsHimmel, D.M. / Mui, S. / O'Neall-Hennessey, E. / Szent-Gyorgyi, A. / Cohen, C.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: The on-off switch in regulated myosins: different triggers but related mechanisms.
Authors: Himmel, D.M. / Mui, S. / O'Neall-Hennessey, E. / Szent-Gyorgyi, A.G. / Cohen, C.
#1: Journal: Structure / Year: 1996
Title: Structure of the Regulatory Domain of Scallop Myosin at 2 Resolution:Implications for Regulation.
Authors: Houdusse, A. / Cohen, C.
#2: Journal: Nature / Year: 1994
Title: Structure of the Regulatory Domain of Scallop Myosin at 2.8 Resolution.
Authors: Xie, X. / Harrison, D.H. / Schlichting, I. / Sweet, R.M. / Kalabokis, V.N. / Szent-Gy rgyi, A. / Cohen, C.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin heavy chain, striated adductor muscle
B: Myosin regulatory light chain, striated adductor muscle
C: Myosin essential light chain, striated adductor muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3064
Polymers43,2813
Non-polymers241
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-73 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 52.780, 58.510
Angle α, β, γ (deg.)113.36, 91.56, 100.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Myosin heavy chain, striated adductor muscle / Myosin


Mass: 8128.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P24733
#2: Protein Myosin regulatory light chain, striated adductor muscle / R-LC


Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P13543
#3: Protein Myosin essential light chain, striated adductor muscle / E-LC / Sulfhydryl light chain / SHLC


Mass: 17591.625 Da / Num. of mol.: 1 / Mutation: D19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians (bay scallop) / Plasmid: pMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P07291
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 100 mM bicine pH 8.3, 45 mM ammonium sulfate, 5 mM magnesium chloride, 2.5 mM EGTA, 3.0 mM sodium azide, 15% (wt/vol) PEG 4000, 4% (vol/vol) PEG 200, 6% (wt/vol) 2,3-butanediol, Hanging drop ...Details: 100 mM bicine pH 8.3, 45 mM ammonium sulfate, 5 mM magnesium chloride, 2.5 mM EGTA, 3.0 mM sodium azide, 15% (wt/vol) PEG 4000, 4% (vol/vol) PEG 200, 6% (wt/vol) 2,3-butanediol, Hanging drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.57→37 Å / Num. all: 15190 / Num. obs: 13187 / % possible obs: 90.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.45 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.064 / Net I/σ(I): 12.298

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDC

1wdc


Resolution: 2.57→34.89 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.819 / Data cutoff high absF: 186917 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 640 4.9 %RANDOM
Rwork0.233 ---
all0.2329 14936 --
obs0.2329 12934 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.68 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso max: 130 Å2 / Biso mean: 48.652 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å2-5.68 Å2-0.27 Å2
2---4.1 Å2-1.25 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.57→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 1 58 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_mcangle_it3.322
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it5.032.5
LS refinement shellResolution: 2.57→2.73 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.436 57 4 %
Rwork0.315 1356 -
all-1413 -
obs--58.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top

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