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- PDB-1kk7: SCALLOP MYOSIN IN THE NEAR RIGOR CONFORMATION -

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Basic information

Entry
Database: PDB / ID: 1kk7
TitleSCALLOP MYOSIN IN THE NEAR RIGOR CONFORMATION
Components
  • MYOSIN ESSENTIAL LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
  • MYOSIN HEAVY CHAIN, STRIATED MUSCLE
  • MYOSIN REGULATORY LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
KeywordsCONTRACTILE PROTEIN / Near rigor / Myosin / Mechanics of MOTOR / nucleotide free
Function / homology
Function and homology information


muscle myosin complex / myosin filament / myosin II complex / myosin complex / sarcomere organization / microfilament motor activity / myofibril / muscle contraction / actin filament binding / calmodulin binding ...muscle myosin complex / myosin filament / myosin II complex / myosin complex / sarcomere organization / microfilament motor activity / myofibril / muscle contraction / actin filament binding / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / : / EF-hand domain / Kinesin motor domain / Kinesin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain ...Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / : / EF-hand domain / Kinesin motor domain / Kinesin / 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 / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / 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: 3.2 Å
AuthorsHimmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: THREE CONFORMATIONAL STATES OF SCALLOP S1
Authors: HOUDUSSE, A. / SZENT-GYORGYI, A.G. / COHEN, C.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: ATOMIC STRUCTURE OFSCALLOP MYOSIN SUBFRAGMENT S1 COMPLEXED WITH MGADP: A NOVEL CONFORMATION OF THE MYOSIN HEAD.
Authors: HOUDUSSE, A. / KALABOKIS, V.N. / HIMMEL, D. / SZENT-GYORGYI, A.G. / COHEN, C.
History
DepositionDec 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 16, 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_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.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_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, STRIATED MUSCLE
Y: MYOSIN REGULATORY LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
Z: MYOSIN ESSENTIAL LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9257
Polymers130,7403
Non-polymers1854
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-107 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.849, 51.227, 84.073
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules AYZ

#1: Protein MYOSIN HEAVY CHAIN, STRIATED MUSCLE / SCALLOP MYOSIN S1


Mass: 95543.750 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P24733
#2: Protein MYOSIN REGULATORY LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE / R-LC


Mass: 17560.855 Da / Num. of mol.: 1 / Fragment: REGULATORY LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P13543
#3: Protein MYOSIN ESSENTIAL LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE / E-LC


Mass: 17635.635 Da / Num. of mol.: 1 / Fragment: ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P07291

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Non-polymers , 4 types, 14 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.: 2 / 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.: 10 / 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: 3.33 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 5000, ammonium sulphate, MgCl2, gycerol, cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4.0 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 mg/mlprotein1drop
220 mMsodium cacodylate1reservoirpH6.3
350.0 mMammonium sulfate1reservoir
42.0 mM1reservoirMgCl2
58 %glycerol1reservoir
610 %(w/v)PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2000
RadiationMonochromator: Rh coated with Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 22975 / Num. obs: 20489 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 61.3 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1482 / Rsym value: 0.335 / % possible all: 65.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 20298 / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 65.8 % / Rmerge(I) obs: 0.335

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFK

1dfk


Resolution: 3.2→48.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2184630.18 / Data cutoff high rms absF: 2184630.18 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1401 7.3 %RANDOM
Rwork0.259 ---
all0.263 20489 --
obs0.263 19088 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 161.96 Å2 / ksol: 0.312598 e/Å3
Displacement parametersBiso mean: 84.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.41 Å20 Å2-2.87 Å2
2---23.4 Å20 Å2
3---37.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 8 10 8147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 157 7.1 %
Rwork0.271 2064 -
obs-2821 64.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor all: 0.263 / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / Rfactor Rwork: 0.271

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