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- PDB-1dfl: SCALLOP MYOSIN S1 COMPLEXED WITH MGADP:VANADATE-TRANSITION STATE -

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Entry
Database: PDB / ID: 1dfl
TitleSCALLOP MYOSIN S1 COMPLEXED WITH MGADP:VANADATE-TRANSITION STATE
Components(MYOSIN HEAD) x 3
KeywordsCONTRACTILE PROTEIN / MYOSIN MOTOR / CONFORMATIONAL CHANGES
Function / homologyMyosin IQ motif-containing domain superfamily / Myosin S1 fragment, N-terminal / EF-hand domain / Myosin N-terminal SH3-like domain / Myosin tail / Myosin head (motor domain) / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / IQ motif profile. / EF-Hand 1, calcium-binding site ...Myosin IQ motif-containing domain superfamily / Myosin S1 fragment, N-terminal / EF-hand domain / Myosin N-terminal SH3-like domain / Myosin tail / Myosin head (motor domain) / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / IQ motif profile. / EF-Hand 1, calcium-binding site / EF-hand domain pair / Myosin, N-terminal, SH3-like / EF-hand calcium-binding domain. / Myosin tail / EF-hand domain / Myosin head, motor domain / IQ motif, EF-hand binding site / EF-hand calcium-binding domain profile. / Myosin motor domain profile. / Myosin N-terminal SH3-like domain profile. / EF-hand domain pair / myosin filament / myosin complex / myofibril / motor activity / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / Myosin essential light chain, striated adductor muscle / Myosin regulatory light chain, striated adductor muscle / Myosin heavy chain, striated muscle
Function and homology information
Specimen sourceArgopecten irradians (bay scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 4.2 Å resolution
AuthorsHoudusse, A. / Szent-Gyorgyi, A.G. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Three conformational states of scallop myosin S1.
Authors: Houdusse, A. / Szent-Gyorgyi, A.G. / Cohen, C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Atomic Structure of Scallop 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.
#2: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 19, 1999 / Release: Oct 25, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 31, 2018Structure modelExperimental preparationexptl_crystal_grow_exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN HEAD
Y: MYOSIN HEAD
Z: MYOSIN HEAD
B: MYOSIN HEAD
W: MYOSIN HEAD
X: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,10816
Polyers255,8466
Non-polymers1,26210
Water0
1
A: MYOSIN HEAD
Y: MYOSIN HEAD
Z: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polyers127,9233
Non-polymers6315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOSIN HEAD
W: MYOSIN HEAD
X: MYOSIN HEAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polyers127,9233
Non-polymers6315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)53.032, 243.475, 124.650
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 3 types, 6 molecules ABYWZX

#1: Protein/peptide MYOSIN HEAD /


Mass: 94843.883 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source: (natural) Argopecten irradians (bay scallop) / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P24733
#2: Protein/peptide MYOSIN HEAD /


Mass: 15914.102 Da / Num. of mol.: 2 / Fragment: REGULATORY LIGHT CHAIN / Source: (natural) Argopecten irradians (bay scallop) / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P13543
#3: Protein/peptide MYOSIN HEAD /


Mass: 17165.070 Da / Num. of mol.: 2 / Fragment: ESSENTIAL LIGHT CHAIN / Source: (natural) Argopecten irradians (bay scallop) / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P07291

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Non-polymers , 4 types, 10 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#5: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Formula: VO4 / Vanadate
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.09 / Density percent sol: 60.25 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
120 mg/mlprotein1drop
250 mMcacodylate1reservoir
350 mMammonium sulfate1reservoir
410 mM1reservoirMgCl2
515 %(v/v)glycerol1reservoir
67 %(v/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE A1 / Synchrotron site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorDetector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 3 Å2 / D resolution high: 3.8 Å / D resolution low: 4 Å / Number obs: 426824 / Rmerge I obs: 0.098 / NetI over sigmaI: 20.4 / Percent possible obs: 95.5
Reflection shellRmerge I obs: 0.216 / Highest resolution: 3.8 Å / Lowest resolution: 3.87 Å / Redundancy: 2.5 % / Percent possible all: 80.9
Reflection
*PLUS
D resolution high: 3.8 Å / D resolution low: 4 Å / B iso Wilson estimate: 3 Å2 / Number obs: 29173 / Number measured all: 426824
Reflection shell
*PLUS
Percent possible obs: 80.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefineDetails: AT THIS RESOLUTION, WE PERFORMED ONLY A RIGID BODY REFINEMENT. NO POSITIONAL REFINEMENT WAS DONE.
Sigma F: 1
Least-squares processR factor R free: 0.4 / R factor R work: 0.394 / R factor obs: 0.394 / Highest resolution: 4.2 Å / Lowest resolution: 2 Å / Number reflection R free: 1128 / Number reflection obs: 22179 / Percent reflection obs: 95
Refine hist #LASTHighest resolution: 4.2 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 10430 / Nucleic acid: 0 / Ligand: 70 / Solvent: 0 / Total: 10500
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
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_deg2.30
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Software
*PLUS
Name: CNS / Classification: refinement
Least-squares process
*PLUS
Highest resolution: 3.8 Å

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