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- PDB-3swb: Crystal structure of the amino-terminal domain of human cardiac t... -

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Basic information

Entry
Database: PDB / ID: 3swb
TitleCrystal structure of the amino-terminal domain of human cardiac troponin C in complex with cadmium at 1.7 A resolution
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsCONTRACTILE PROTEIN / HELIX-LOOP-HELIX EF-HAND MOTIF / CALCIUM SENSOR / CADMIUM BINDING
Function / homology
Function and homology information


diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / response to metal ion ...diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding / calcium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
EF-hand domain pair / 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
Similarity search - Domain/homology
ACETATE ION / : / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsZhang, X.L. / Paetzel, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of cardiac troponin C regulatory domain with bound Cd(2+) reveals a closed conformation and unique ion coordination.
Authors: Zhang, X.L. / Tibbits, G.F. / Paetzel, M.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Advisory / Author supporting evidence / Refinement description
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms / software
Item: _software.name
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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_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, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,92411
Polymers10,0701
Non-polymers85410
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.793, 49.793, 117.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-92-

CA

21A-111-

HOH

DetailsGel-filtration and light scattering data shows Monomer

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Components

#1: Protein Troponin C, slow skeletal and cardiac muscles / / TN-C


Mass: 10070.304 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC, TNNC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63316
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: cadmium sulphate octahydrate 0.02M, sodium acetate 0.6M, 0.1M Tris , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 5, 2011
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 10707 / Num. obs: 10699 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 35.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 102.75
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 11.63 / Num. unique all: 1039 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL2Mapmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.67→43.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.595 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16456 509 4.8 %RANDOM
Rwork0.13474 ---
obs0.13622 10090 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.744 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å21.19 Å20 Å2
2--2.37 Å20 Å2
3----3.56 Å2
Refinement stepCycle: LAST / Resolution: 1.67→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 13 45 738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.991931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.093584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.37427.36838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56315140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.018152
X-RAY DIFFRACTIONr_chiral_restr0.1240.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02525
X-RAY DIFFRACTIONr_mcbond_it2.551.5441
X-RAY DIFFRACTIONr_mcangle_it3.8822689
X-RAY DIFFRACTIONr_scbond_it5.7113284
X-RAY DIFFRACTIONr_scangle_it8.2474.5242
X-RAY DIFFRACTIONr_rigid_bond_restr3.2023725
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.147 33 -
Rwork0.116 733 -
obs--99.87 %

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