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- PDB-3u59: N-terminal 98-aa fragment of smooth muscle tropomyosin beta -

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Basic information

Entry
Database: PDB / ID: 3u59
TitleN-terminal 98-aa fragment of smooth muscle tropomyosin beta
ComponentsTropomyosin beta chain
KeywordsCONTRACTILE PROTEIN / Muscle contraction / Actin
Function / homology
Function and homology information


muscle contraction / actin filament / actin filament organization / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity / identical protein binding / 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 beta chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJampani, N. / Dominguez, R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural analysis of smooth muscle tropomyosin alpha and beta isoforms.
Authors: Rao, J.N. / Rivera-Santiago, R. / Li, X.E. / Lehman, W. / Dominguez, R.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tropomyosin beta chain
B: Tropomyosin beta chain
C: Tropomyosin beta chain
D: Tropomyosin beta chain


Theoretical massNumber of molelcules
Total (without water)46,2884
Polymers46,2884
Non-polymers00
Water2,198122
1
A: Tropomyosin beta chain
B: Tropomyosin beta chain


Theoretical massNumber of molelcules
Total (without water)23,1442
Polymers23,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-44 kcal/mol
Surface area15430 Å2
MethodPISA
2
C: Tropomyosin beta chain

C: Tropomyosin beta chain


Theoretical massNumber of molelcules
Total (without water)23,1442
Polymers23,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area4160 Å2
ΔGint-40 kcal/mol
Surface area15160 Å2
MethodPISA
3
D: Tropomyosin beta chain

D: Tropomyosin beta chain


Theoretical massNumber of molelcules
Total (without water)23,1442
Polymers23,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4160 Å2
ΔGint-47 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.121, 75.711, 137.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Tropomyosin beta chain / Beta-tropomyosin / Tropomyosin-2


Mass: 11571.923 Da / Num. of mol.: 4 / Fragment: unp residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TPM2 / Plasmid: PRSF-Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19352
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES, 5 mM CaCl2, 28-31 % 2- methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→29 Å / Num. all: 20821 / Num. obs: 20734 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.0706 / Net I/σ(I): 15.82
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.63 % / Rmerge(I) obs: 0.5048 / Mean I/σ(I) obs: 2.98 / Num. unique all: 2445 / % possible all: 100

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Processing

Software
NameVersionClassification
JDirector(Rigaku)data collection
SHELXDphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→29 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.696 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 4.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33667 14902 95 %RANDOM
Rwork0.29453 ---
obs0.33465 15687 100 %-
all-2880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.004 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--1.04 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 0 122 3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9964248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2285404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08327.931174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.78715756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5481516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022328
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7951.51997
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.06223161
X-RAY DIFFRACTIONr_scbond_it10.65731208
X-RAY DIFFRACTIONr_scangle_it13.324.51083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 976 -
Rwork0.43 52 -
obs--100 %

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