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- PDB-3jvt: Calcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with R... -

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Basic information

Entry
Database: PDB / ID: 3jvt
TitleCalcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with Reconstituted Complete Light Chains
Components
  • Myosin essential light chain, striated adductor muscle
  • Myosin heavy chain, striated adductor muscle
  • Myosin regulatory light chain, striated adductor muscle
KeywordsCONTRACTILE PROTEIN / Regulated myosins / smooth and molluscan muscle / X-ray crystallographic structure / scallop regulatory domain/lever arm / on-state / calcium-binding protein / 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


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
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, 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. / 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 / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Few Secondary Structures / Irregular / EF-hand calcium-binding domain profile. / EF-hand domain / 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: 2.1 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 A 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 A Resolution.
Authors: Xie, X. / Harrison, D.H. / Schlichting, I. / Sweet, R.M. / Kalabokis, V.N. / Szent-Gyorgyi, A. / Cohen, C.
History
DepositionSep 17, 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: Refinement description / Category: software
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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, 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)43,3905
Polymers43,3253
Non-polymers642
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-84 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.710, 52.230, 55.250
Angle α, β, γ (deg.)65.300, 66.400, 70.240
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Myosin heavy chain, striated adductor muscle


Mass: 8128.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / 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 / Details: Bay Scallop / 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: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291

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Non-polymers , 3 types, 249 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


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 150 mM HEPES pH 7.0, 50 mM Ammonium Sulfate, 0.5 mM Calcium Chloride, 5 mM Magnesium Chloride, 5 mM Sodium Azide, 16.5% (wt/vol) PEG 4000 combined with equal volume of 16.9 mg/ml protein in ...Details: 150 mM HEPES pH 7.0, 50 mM Ammonium Sulfate, 0.5 mM Calcium Chloride, 5 mM Magnesium Chloride, 5 mM Sodium Azide, 16.5% (wt/vol) PEG 4000 combined with equal volume of 16.9 mg/ml protein in 5 mM HEPES pH 7, 20 mM NaCl, 2 mM Magnesium Chloride, 0.2 mM Calcium Chloride, 0.1 mM EGTA, 3.0 mM Sodium Azide, Hanging drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 1996
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 26353 / Num. obs: 25062 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1wdc


Resolution: 2.1→9.99 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.856 / Data cutoff high absF: 160980 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 2284 10 %RANDOM
Rwork0.2067 ---
all0.2091 24632 --
obs0.2091 22939 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.703 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 119.93 Å2 / Biso mean: 33.04 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å22.65 Å2-2.7 Å2
2---1.43 Å2-2.15 Å2
3----1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 2 247 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it2.281.5
X-RAY DIFFRACTIONc_mcangle_it3.522
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_scangle_it5.842.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 318 9.3 %
Rwork0.222 3104 -
all-3422 -
obs--81.6 %
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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