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- PDB-1ncy: TROPONIN-C, COMPLEX WITH MANGANESE -

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Basic information

Entry
Database: PDB / ID: 1ncy
TitleTROPONIN-C, COMPLEX WITH MANGANESE
ComponentsTROPONIN C
KeywordsCALCIUM-BINDING PROTEIN / MUSCLE PROTEIN
Function / homology
Function and homology information


troponin complex / Striated Muscle Contraction / skeletal muscle contraction / calcium ion binding
Similarity search - Function
EF hand / 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 / 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: 2.1 Å
AuthorsSundaralingam, M. / Rao, S.T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-ray structures of Mn, Cd and Tb metal complexes of troponin C.
Authors: Rao, S.T. / Satyshur, K.A. / Greaser, M.L. / Sundaralingam, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structure of Chicken Skeletal Muscle Troponin-C at 1.78 Angstroms Resolution
Authors: Satyshur, K.A. / Pyzalska, D. / Rao, S.T. / Greaser, M. / Sundaralingam, M.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Refined Structure of Chicken Skeletal Muscle Troponin C in the Two-Calcium State at 2-A Resolution
Authors: Satyshur, K.A. / Rao, S.T. / Pyzalska, D. / Drendel, W. / Greaser, M. / Sundaralingam, M.
#3: 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.
#4: 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.
#5: Journal: FEBS Lett. / Year: 1976
Title: The Amino Acid Sequence of Troponin C from Chicken Skeletal Muscle
Authors: Wilkinson, J.M.
History
DepositionJun 2, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: 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)18,4674
Polymers18,2611
Non-polymers2063
Water1,892105
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

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Components

#1: Protein TROPONIN C


Mass: 18261.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: SKELETAL / Tissue: SKELETAL MUSCLE / References: UniProt: P02588
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 105 / 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
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein1drop
230 %satammonium sulfate1drop
350 mMsodium acetate1reservoir
45 mM1reservoirMnCl2
51 mM1reservoirNaN3
643 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 29532 / % possible obs: 69 % / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
PROLSQrefinement
PURDUEDATA PROCESSING PACKAGEdata reduction
PURDUEDATA PROCESSING PACKAGEdata scaling
RefinementResolution: 2.1→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.13 -
obs-6380
Displacement parametersBiso mean: 21.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 7 124 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0040.01
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.34
X-RAY DIFFRACTIONp_mcangle_it5.66
X-RAY DIFFRACTIONp_scbond_it3.34
X-RAY DIFFRACTIONp_scangle_it5.66
X-RAY DIFFRACTIONp_plane_restr0.0040.01
X-RAY DIFFRACTIONp_chiral_restr0.0335
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.55
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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