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- PDB-1c1g: CRYSTAL STRUCTURE OF TROPOMYOSIN AT 7 ANGSTROMS RESOLUTION IN THE... -

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Basic information

Entry
Database: PDB / ID: 1c1g
TitleCRYSTAL STRUCTURE OF TROPOMYOSIN AT 7 ANGSTROMS RESOLUTION IN THE SPERMINE-INDUCED CRYSTAL FORM
ComponentsTROPOMYOSIN
KeywordsCONTRACTILE PROTEIN / TROPOMYOSIN COILED-COIL ALPHA-HELICAL
Function / homology
Function and homology information


cardiac muscle contraction / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin
Similarity search - Domain/homology
Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 7 Å
AuthorsWhitby, F.G. / Phillips Jr., G.N.
CitationJournal: Proteins / Year: 2000
Title: Crystal structure of tropomyosin at 7 Angstroms resolution.
Authors: Whitby, F.G. / Phillips Jr., G.N.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROPOMYOSIN
B: TROPOMYOSIN
C: TROPOMYOSIN
D: TROPOMYOSIN


Theoretical massNumber of molelcules
Total (without water)131,1394
Polymers131,1394
Non-polymers00
Water00
1
A: TROPOMYOSIN
B: TROPOMYOSIN


Theoretical massNumber of molelcules
Total (without water)65,5692
Polymers65,5692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-127 kcal/mol
Surface area42200 Å2
MethodPISA
2
C: TROPOMYOSIN
D: TROPOMYOSIN


Theoretical massNumber of molelcules
Total (without water)65,5692
Polymers65,5692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-130 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.738, 55.300, 136.259
Angle α, β, γ (deg.)90, 97.415, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TROPOMYOSIN


Mass: 32784.637 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: CARDIAC MUSCLE / References: UniProt: P42639

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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: 3.7 Å3/Da / Density % sol: 68 %
Description: Thimerosal was pre-reacted with purified tropomyosin prior growing crystals (spermine-induced crystal form). One mercury reacts with cyteine-190 of each chain of the molecule. Thus four ...Description: Thimerosal was pre-reacted with purified tropomyosin prior growing crystals (spermine-induced crystal form). One mercury reacts with cyteine-190 of each chain of the molecule. Thus four mercury atoms are present in the asymmetric unit. Two mercury atoms are located adjecent to each other on neighboring chains on the molecule, and for heavy-atom phasing purposes, these pairs were considered as a single point scatterer (due to 7 angstrom resolution limit). SIR phases determined from this derivative showed clear molecular packing consistent with the previously determined 9 angstrom structure in the same crystal form which was determined by molecular replacement using a highly simplified model (Whitby, et al. JMB 1992;227:441-452)
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 7.4
Details: SPERMINE, pH 7.4, LIQUID DIFFUSION, temperature 18K
Crystal grow
*PLUS
Temperature: 15-17.5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 mg/mlprotein11
20.040-0.065 Mspermine11
30.070 Mspermine12

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Data collection

DiffractionMean temperature: 21 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.000, 1.54
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541
ReflectionResolution: 7→100 Å / Num. obs: 3117 / % possible obs: 96.38 % / Observed criterion σ(I): 0 / Redundancy: 3.4 %

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Processing

Software
NameClassification
XTALVIEWrefinement
X-PLORrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SIR / Resolution: 7→100 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.404 --
obs-3117 96.38 %
Refinement stepCycle: LAST / Resolution: 7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9160 0 0 0 9160
LS refinement shellResolution: 7→7.25 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.477 285 -
obs--94.06 %

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