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- PDB-1sr6: Structure of nucleotide-free scallop myosin S1 -

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Basic information

Entry
Database: PDB / ID: 1sr6
TitleStructure of nucleotide-free scallop myosin S1
Components
  • Myosin essential light chain, striated adductor muscle
  • Myosin heavy chain, striated muscle
  • Myosin regulatory light chain, striated adductor muscle
KeywordsCONTRACTILE PROTEIN / scallop myosin S1 / near rigor / complex salt bridge / novel conformation of nucleotide
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
Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 ...Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 / Methane Monooxygenase Hydroxylase; Chain G, 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 / EF-hand domain pair / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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 / Resolution: 2.75 Å
AuthorsRisal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Myosin subfragment 1 structures reveal a partially bound nucleotide and a complex salt bridge that helps couple nucleotide and actin binding.
Authors: Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C.
#1: Journal: Structure / Year: 2003
Title: Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head
Authors: Gourinath, S. / Himmel, D.M. / Brown, J.H. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Cohen, C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor
Authors: Himmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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

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Assembly

Deposited unit
A: Myosin heavy chain, striated 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)131,1726
Polymers131,0123
Non-polymers1603
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-94 kcal/mol
Surface area53550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.591, 51.109, 162.329
Angle α, β, γ (deg.)90.00, 98.02, 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 Myosin heavy chain, striated muscle


Mass: 95815.062 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: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291

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Non-polymers , 4 types, 98 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6% PEG 8000, 50mM ammonium sulfate, 8% glycerol, 10mM magnesium chloride, 50mM sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.75→38.79 Å / Num. all: 38495 / Num. obs: 31951 / % possible obs: 83 % / Observed criterion σ(F): -3 / Redundancy: 4 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 20.5
Reflection shellResolution: 2.75→2.92 Å / Num. unique all: 3901 / Rsym value: 0.385

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1kk7

1kk7


Resolution: 2.75→38.79 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 485766.54 / 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
Rfree0.286 1511 5.1 %RANDOM
Rwork0.242 ---
all0.242 ---
obs0.242 31951 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3919 Å2 / ksol: 0.338759 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1-6.01 Å20 Å2-5.15 Å2
2---6.89 Å20 Å2
3---0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.43 Å
Luzzati d res low-39.79 Å
Luzzati sigma a0.57 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.75→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 7 95 8895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it2.631.5
X-RAY DIFFRACTIONc_mcangle_it4.492
X-RAY DIFFRACTIONc_scbond_it6.882
X-RAY DIFFRACTIONc_scangle_it9.452.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 239 5.8 %
Rwork0.342 3901 -
obs-3901 69.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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