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- PDB-1top: STRUCTURE OF CHICKEN SKELETAL MUSCLE TROPONIN-C AT 1.78 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1top
TitleSTRUCTURE OF CHICKEN SKELETAL MUSCLE TROPONIN-C AT 1.78 ANGSTROMS RESOLUTION
ComponentsTROPONIN C
KeywordsCONTRACTILE SYSTEM PROTEIN
Function / homology
Function and homology information


Striated Muscle Contraction / troponin complex / skeletal muscle contraction / calcium ion binding
Similarity search - Function
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsSundaralingam, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structure of chicken skeletal muscle troponin C at 1.78 A resolution.
Authors: Satyshur, K.A. / Pyzalska, D. / Greaser, M. / Rao, S.T. / Sundaralingam, M.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Refined Structure of Chicken Skeletal Muscle Troponin C in the Two-Calcium State at 2-Angstroms Resolution
Authors: Satyshur, K.A. / Rao, S.T. / Pyzalska, D. / Drendel, W. / Greaser, M. / Sundaralingam, M.
#2: Journal: Science / Year: 1985
Title: Molecular Structure of Troponin C from Chicken Skeletal Muscle at 3-Angstrom Resolution
Authors: Sundaralingam, M. / Bergstrom, R. / Strasburg, G. / Rao, S.T. / Roychowdhury, P. / Greaser, M. / Wang, B.C.
#3: Journal: J.Biol.Chem. / Year: 1980
Title: X-Ray Diffraction Studies of Troponin-C Crystals from Rabbit and Chicken Skeletal Muscles
Authors: Strasburg, G.M. / Greaser, M.L. / Sundaralingam, M.
#4: Journal: FEBS Lett. / Year: 1976
Title: The Amino Acid Sequence of Troponin C from Chicken Skeletal Muscle
Authors: Wilkinson, J.M.
History
DepositionAug 11, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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.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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: TROPONIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4374
Polymers18,2611
Non-polymers1763
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.700, 66.700, 60.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: GLU 159 - GLY 160 OMEGA ANGLE = 144.906 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein TROPONIN C


Mass: 18261.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P02588
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mgprotein1drop
26 Murea1reservoir
350 mMTris-HCl1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 8 Å / Num. all: 15168 / Num. obs: 14788 / % possible obs: 97.5 % / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.168 / Rfactor obs: 0.168 / Highest resolution: 1.78 Å
Refinement stepCycle: LAST / Highest resolution: 1.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 7 164 1464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 8 Å / Num. reflection all: 15168 / Num. reflection obs: 14788 / σ(F): 3 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d2.3
X-RAY DIFFRACTIONx_dihedral_angle_d20.6
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_mcbond_it6.45
X-RAY DIFFRACTIONx_scbond_it8.26
X-RAY DIFFRACTIONx_mcangle_it7.87
X-RAY DIFFRACTIONx_scangle_it9.28.5
LS refinement shell
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 1.8 Å / Num. reflection Rfree: 449 / Total num. of bins used: 12 / Num. reflection obs: 526

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