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- PDB-5tnc: REFINED CRYSTAL STRUCTURE OF TROPONIN C FROM TURKEY SKELETAL MUSC... -

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Basic information

Entry
Database: PDB / ID: 5tnc
TitleREFINED CRYSTAL STRUCTURE OF TROPONIN C FROM TURKEY SKELETAL MUSCLE AT 2.0 ANGSTROMS RESOLUTION
ComponentsTROPONIN-C
KeywordsCONTRACTILE SYSTEM PROTEINS
Function / homology
Function and homology information


myosin II complex / calcium ion binding
Similarity search - Function
EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Troponin C, skeletal muscle
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHerzberg, O. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 A resolution.
Authors: Herzberg, O. / James, M.N.
#1: Journal: Methods Enzymol. / Year: 1987
Title: Molecular Structure of Troponin C and its Implications for the Ca2+ Triggering of Muscle Contraction
Authors: Herzberg, O. / Moult, J. / James, M.N.G.
#2: Journal: Calcium-Binding Proteins in Health and Disease / Year: 1987
Title: Conformational Flexibility of Troponin C
Authors: Herzberg, O. / Moult, J. / James, M.N.G.
#3: Journal: Ciba Found.Symp. / Year: 1986
Title: Calcium Binding to Skeletal Muscle Troponin C and the Regulation of Muscle Contraction
Authors: Herzberg, O. / Moult, J. / James, M.N.G.
#4: Journal: FEBS Lett. / Year: 1986
Title: Crystallographic Determination of Lanthanide Ion Binding to Troponin C
Authors: Herzberg, O. / James, M.N.G.
#5: Journal: J.Biol.Chem. / Year: 1986
Title: A Model for the Ca2+-Induced Conformational Transition of Troponin C. A Trigger for Muscle Contraction
Authors: Herzberg, O. / Moult, J. / James, M.N.G.
#6: Journal: Biochemistry / Year: 1985
Title: Common Structural Framework of the Two Ca2+(Slash)Mg2+ Binding Loops of Troponin C and Other Ca2+ Binding Proteins
Authors: Herzberg, O. / James, M.N.G.
#7: Journal: Nature / Year: 1985
Title: Structure of the Calcium Regulatory Muscle Protein Troponin-C at 2.8 Angstroms Resolution
Authors: Herzberg, O. / James, M.N.G.
#8: Journal: J.Mol.Biol. / Year: 1984
Title: Crystallographic Data for Troponin C from Turkey Skeletal Muscle
Authors: Herzberg, O. / Hayakawa, K. / James, M.N.G.
#9: Journal: Acta Crystallogr.,Sect.A / Year: 1984
Title: The Crystal Structure of Troponin C from Turkey Skeletal Muscle at 2.8 Angstroms Resolution
Authors: Herzberg, O. / James, M.N.G.
History
DepositionMay 27, 1988Processing site: BNL
SupersessionOct 9, 1988ID: 2TNC
Revision 1.0Oct 9, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROPONIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4003
Polymers18,3201
Non-polymers802
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.550, 66.550, 60.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: SEE REMARK 4. / 2: SEE REMARK 6.

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Components

#1: Protein TROPONIN-C


Mass: 18320.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / References: UniProt: P10246
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE WATER MOLECULES ARE ARRANGED IN DESCENDING ORDER OF RELIABILITY WHERE RELIABILITY IS DEFINED BY ...THE WATER MOLECULES ARE ARRANGED IN DESCENDING ORDER OF RELIABILITY WHERE RELIABILITY IS DEFINED BY THE QUALITY FACTOR OCCUPANCY**2/B (M.N.G.JAMES, A.R.SIELECKI, J.MOL. BIOL., V. 163, P. 299 (1983)). THUS A QUALITY FACTOR OF 0.025 CORRESPONDS TO B=40.0 AND OCCUPANCY=1.0.
Sequence detailsBASED ON AMINO ACID COMPOSITION AND THE ELECTRON DENSITY MAP, ALA 99 IN CHICKEN TNC WAS IDENTIFIED ...BASED ON AMINO ACID COMPOSITION AND THE ELECTRON DENSITY MAP, ALA 99 IN CHICKEN TNC WAS IDENTIFIED AS GLU 99 IN TURKEY TNC.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal grow
*PLUS
Method: unknown / PH range low: 5 / PH range high: 4.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 %satammonium sulfate1drop
2100 mMsodium acetate1reservoir
310 mM1reservoirCaCl2
42.5-5.0 %(v/v)PEG2001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 8054 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06 / Num. measured all: 10825

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.155 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 2 157 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.017
X-RAY DIFFRACTIONp_angle_d0.0450.028
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.034
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0120.015
X-RAY DIFFRACTIONp_chiral_restr0.1980.14
X-RAY DIFFRACTIONp_singtor_nbd0.2390.4
X-RAY DIFFRACTIONp_multtor_nbd0.2860.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2830.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.53.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 8054 / σ(I): 2 / Highest resolution: 2 Å / Lowest resolution: 10 Å / Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS

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