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- PDB-1a2x: COMPLEX OF TROPONIN C WITH A 47 RESIDUE (1-47) FRAGMENT OF TROPONIN I -

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Basic information

Entry
Database: PDB / ID: 1a2x
TitleCOMPLEX OF TROPONIN C WITH A 47 RESIDUE (1-47) FRAGMENT OF TROPONIN I
Components
  • TROPONIN C
  • TROPONIN I
KeywordsCOMPLEX (SKELETAL MUSCLE/MUSCLE PROTEIN) / TROPONIN / MUSCLE CONTRACTION REGULATION / COMPLEX (SKELETAL MUSCLE-MUSCLE PROTEIN) / COMPLEX (SKELETAL MUSCLE-MUSCLE PROTEIN) complex
Function / homology
Function and homology information


troponin T binding / troponin complex / myosin II complex / skeletal muscle contraction / cardiac muscle contraction / actin binding / calcium ion binding
Similarity search - Function
: / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...: / Troponin / Troponin domain superfamily / Troponin / 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 / Troponin I, fast skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR/MAD / Resolution: 2.3 Å
AuthorsVassylyev, D.G. / Takeda, S. / Wakatsuki, S. / Maeda, K. / Maeda, Y.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of troponin C in complex with troponin I fragment at 2.3-A resolution.
Authors: Vassylyev, D.G. / Takeda, S. / Wakatsuki, S. / Maeda, K. / Maeda, Y.
#1: Journal: Protein Sci. / Year: 1997
Title: Production, Crystallization, and Preliminary X-Ray Analysis of Rabbit Skeletal Muscle Troponin Complex Consisting of Troponin C and Fragment (1-47) of Troponin I
Authors: Saijo, Y. / Takeda, S. / Scherer, A. / Kobayashi, T. / Maeda, Y. / Taniguchi, H. / Yao, M. / Wakatsuki, S.
History
DepositionJan 13, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_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
B: TROPONIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6084
Polymers23,5282
Non-polymers802
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-29 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.900, 46.900, 152.300
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: 17981.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: FAST SKELETAL MUSCLE / Organ: SKELETAL / Plasmid: PMALC2 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K / References: UniProt: P02586
#2: Protein/peptide TROPONIN I


Mass: 5546.197 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: FAST SKELETAL MUSCLE / Organ: SKELETAL / Plasmid: PTRC / Cellular location (production host): INCLUSION BODY / Production host: Escherichia coli (E. coli) / Strain (production host): K / References: UniProt: P02643
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.3 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HANGING-DROP VAPOR DIFFUSION METHOD WAS USED AT 289K BY MIXING THE PROTEIN SOLUTION CONTAINING 25-30MG/ML OF THE CI47 COMPLEX WITH A RESERVOIR SOLUTION CONTAINING 1.5M SODIUM CITRATE, 0.1M ...Details: HANGING-DROP VAPOR DIFFUSION METHOD WAS USED AT 289K BY MIXING THE PROTEIN SOLUTION CONTAINING 25-30MG/ML OF THE CI47 COMPLEX WITH A RESERVOIR SOLUTION CONTAINING 1.5M SODIUM CITRATE, 0.1M TRIS-HCL, PH 8.0, 15% TREHALOSE., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Saijo, Y., (1997) Protein Sci., 6, 916.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 mg/mlprotein1drop
21.5 Msodium citrate1reservoir
30.1 MTris-HCl1reservoirpH8.0
415 %trehalose1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 8870 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 94
Reflection
*PLUS
Num. measured all: 37214

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SIR/MAD / Resolution: 2.3→10 Å / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.325 591 7 %RANDOM
Rwork0.222 ---
obs0.222 8736 96.2 %-
Displacement parametersBiso mean: 41 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 2 89 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.91.5
X-RAY DIFFRACTIONx_mcangle_it6.62
X-RAY DIFFRACTIONx_scbond_it4.62
X-RAY DIFFRACTIONx_scangle_it82.5
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.389 58 6.7 %
Rwork0.337 1000 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72

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