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- PDB-1b7t: MYOSIN DIGESTED BY PAPAIN -

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Basic information

Entry
Database: PDB / ID: 1b7t
TitleMYOSIN DIGESTED BY PAPAIN
Components
  • MYOSIN ESSENTIAL LIGHT CHAIN
  • MYOSIN HEAVY CHAINMyosin
  • MYOSIN REGULATORY LIGHT CHAIN
KeywordsMYOSIN / MYOSIN MOTOR
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 / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsHoudusse, A. / Kalabokis, V. / Himmel, D. / Szent-Gyorgyi, A.G. / Cohen, C.
CitationJournal: Cell / Year: 1999
Title: Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head.
Authors: A Houdusse / V N Kalabokis / D Himmel / A G Szent-Györgyi / C Cohen
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 15, 1999 / Release: May 12, 1999
RevisionDateData content typeGroupProviderType
1.0May 12, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN HEAVY CHAIN
Y: MYOSIN REGULATORY LIGHT CHAIN
Z: MYOSIN ESSENTIAL LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0307
Polyers130,5143
Non-polymers5164
Water1,874104
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)9410
ΔGint (kcal/M)-95
Surface area (Å2)49250
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.700, 58.900, 138.900
Angle α, β, γ (deg.)89.10, 90.00, 73.50
Int Tables number1
Cell settingtriclinic
Space group name H-MP 1

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Components

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Protein/peptide , 3 types, 3 molecules AYZ

#1: Protein/peptide MYOSIN HEAVY CHAIN / Myosin


Mass: 95317.430 Da / Num. of mol.: 1 / Fragment: PAPAIN DIGESTED, SUBFRAGMENT 1 (S1) / Source: (natural) Argopecten irradians (bay scallop) / Details: PAPAIN DIGESTION OF MYOSIN / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P24733
#2: Protein/peptide MYOSIN REGULATORY LIGHT CHAIN


Mass: 17560.855 Da / Num. of mol.: 1 / Fragment: PAPAIN DIGESTED, SUBFRAGMENT 1 (S1) / Source: (natural) Argopecten irradians (bay scallop) / Details: PAPAIN DIGESTION OF MYOSIN / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P13543
#3: Protein/peptide MYOSIN ESSENTIAL LIGHT CHAIN


Mass: 17635.635 Da / Num. of mol.: 1 / Fragment: PAPAIN DIGESTED, SUBFRAGMENT 1 (S1) / Source: (natural) Argopecten irradians (bay scallop) / Details: PAPAIN DIGESTION OF MYOSIN / Genus: Argopecten / Tissue: SKELETAL MUSCLE / References: UniProt: P07291

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Non-polymers , 4 types, 108 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Formula: H2O / Water

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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: 3.11 / Density percent sol: 64 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Density percent sol: 64.6 %
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, sitting drop / Details: used to seeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
13 %PEG200001drop
250 mMTris1drop
36 %glycerol1drop
440 mM1dropNaCl
510 mg/mlprotain1drop
62 mMMgADP1drop

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE F1 / Synchrotron site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: CCD / Collection date: Jan 15, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 5 Å2 / D resolution high: 2.5 Å / D resolution low: 4 Å / Number obs: 43838 / Rmerge I obs: 0.048 / Rsym value: 0.048 / NetI over sigmaI: 11.6 / Redundancy: 3 % / Percent possible obs: 80.6
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.8 Å / Number unique obs: 5968 / Percent possible obs: 38.5 / Rmerge I obs: 0.11 / Redundancy: 1.4 % / MeanI over sigI obs: 6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR4.0refinement
CCP4(SCALA)data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMD, 1WDC
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.297 / R factor R work: 0.2244 / Highest resolution: 2.5 Å / Lowest resolution: 3 Å / Number reflection all: 43833 / Number reflection obs: 43833 / Percent reflection R free: 5 / Percent reflection obs: 80.5
Refine analyzeLuzzati sigma a free: 0.43 Å / Luzzati sigma a obs: 0.36 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 8249 / Nucleic acid: 0 / Ligand: 30 / Solvent: 104 / Total: 8383
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.474
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.91
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.461
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 4 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor obs: 0.2244 / Highest resolution: 2.5 Å / Lowest resolution: 3 Å / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.91
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.461

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