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- PDB-1ic2: DECIPHERING THE DESIGN OF THE TROPOMYOSIN MOLECULE -

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Basic information

Entry
Database: PDB / ID: 1ic2
TitleDECIPHERING THE DESIGN OF THE TROPOMYOSIN MOLECULE
ComponentsTROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
KeywordsCONTRACTILE PROTEIN / alpha-helical coiled coil / alanine / symmetry / axial stagger / bend
Function / homology
Function and homology information


Smooth Muscle Contraction / Striated Muscle Contraction / cardiac muscle contraction / cytoskeletal protein binding / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity ...Smooth Muscle Contraction / Striated Muscle Contraction / cardiac muscle contraction / cytoskeletal protein binding / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Tropomyosins signature. / Tropomyosin / Tropomyosin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsBrown, J.H. / Kim, K.-H. / Jun, G. / Greenfield, N.J. / Dominguez, R. / Volkmann, N. / Hitchcock-DeGregori, S.E. / Cohen, C.
Citation
#1: Journal: J.Mol.Biol. / Year: 1969
Title: Tropomyosin: Crystal Structure, Polymorphism and Molecular Interactions
Authors: Caspar, D.L. / Cohen, C. / Longley, W.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Tropomyosin Crystal Structure and Muscle Regulation
Authors: Phillips Jr., G.N. / Fillers, J.P. / Cohen, C.
#3: Journal: Biochemistry / Year: 1998
Title: The Structure of the N-terminus of Striated Muscle alpha-Tropomyosin in a Chimeric Peptide: Nuclear Magnetic Resonance Structure and Circular Dichroism Studies
Authors: Greenfield, N.J. / Montelione, G.T. / Farid, R.S. / Hitchcock-DeGregori, S.E.
#4: Journal: Proteins / Year: 2000
Title: Crystal Structure of Tropomyosin at 7 Angstroms Resolution
Authors: Whitby, F.G. / Phillips Jr., G.N.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
B: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
C: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
D: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE


Theoretical massNumber of molelcules
Total (without water)37,0944
Polymers37,0944
Non-polymers00
Water3,207178
1
A: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
B: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE


Theoretical massNumber of molelcules
Total (without water)18,5472
Polymers18,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-43 kcal/mol
Surface area11520 Å2
MethodPISA
2
C: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE
D: TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE


Theoretical massNumber of molelcules
Total (without water)18,5472
Polymers18,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-43 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.400, 45.500, 56.300
Angle α, β, γ (deg.)93.70, 98.10, 104.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TROPOMYOSIN ALPHA CHAIN, SKELETAL MUSCLE


Mass: 9273.543 Da / Num. of mol.: 4 / Mutation: A81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)PLYS / References: UniProt: P04268
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.6
Details: PEG 200, isopropanol, magnesium chloride, ammonium acetate, TRIS, pH 7.6, VAPOR DIFFUSION, temperature 277K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %PEG2001reservoir
210 %isopropanol1reservoir
316 mM1reservoirMgCl2
470 mMammonium acetate1reservoir
5Tris1reservoir
61

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.908
SYNCHROTRONNSLS X12C21.15
SYNCHROTRONNSLS X12C30.92
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MARRESEARCH2IMAGE PLATE
MARRESEARCH3IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9081
21.151
30.921
ReflectionResolution: 2→50 Å / Num. all: 26797 / Num. obs: 26797 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 10 / % possible all: 99.5
Reflection
*PLUS

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 1326 5 %Random
Rwork0.2488 ---
all-26793 --
obs-26793 99.9 %-
Displacement parametersBiso mean: 43.8603 Å2
Baniso -1Baniso -2Baniso -3
1--6.688 Å20.656 Å2-0.959 Å2
2--9.71 Å27.436 Å2
3----3.022 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 178 2670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.87827
X-RAY DIFFRACTIONc_bond_d0.00658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2-2.070.33221310.2741X-RAY DIFFRACTION2547
2.52-2.710.29611450.2582X-RAY DIFFRACTION2543
2.71-2.990.34791270.2894X-RAY DIFFRACTION2572
2.99-3.420.30141240.2628X-RAY DIFFRACTION2543
3.42-4.310.25851330.2234X-RAY DIFFRACTION2539
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d13.17
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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