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- PDB-1dtl: CRYSTAL STRUCTURE OF CALCIUM-SATURATED (3CA2+) CARDIAC TROPONIN C... -

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Basic information

Entry
Database: PDB / ID: 1dtl
TitleCRYSTAL STRUCTURE OF CALCIUM-SATURATED (3CA2+) CARDIAC TROPONIN C COMPLEXED WITH THE CALCIUM SENSITIZER BEPRIDIL AT 2.15 A RESOLUTION
ComponentsCARDIAC TROPONIN C
KeywordsSTRUCTURAL PROTEIN / helix-turn-helix
Function / homology
Function and homology information


cardiac Troponin complex / Striated Muscle Contraction / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / calcium ion binding
Similarity search - Function
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 / 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
Chem-BEP / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, Y. / Love, M.L. / Putkey, J.A. / Cohen, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Bepridil opens the regulatory N-terminal lobe of cardiac troponin C.
Authors: Li, Y. / Love, M.L. / Putkey, J.A. / Cohen, C.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARDIAC TROPONIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6217
Polymers18,4011
Non-polymers1,2206
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.270, 62.040, 62.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CARDIAC TROPONIN C


Mass: 18401.377 Da / Num. of mol.: 1 / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P09860
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEP / 1-ISOBUTOXY-2-PYRROLIDINO-3[N-BENZYLANILINO] PROPANE / BEPRIDIL


Mass: 366.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H34N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG3350 monodisperse, magnesium chloride, calcium chloride, HEPES, bepridil, HCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMprotein1drop
26 mM1dropCaCl2
32.5 mMbepridil-HCl1drop
410 mMHEPES1drop
530 %PEG33501reservoir
620 mM1reservoirMgCl2
750 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 8025 / Num. obs: 7998 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.83 % / Biso Wilson estimate: 21.63 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 34.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.126 / Num. unique all: 764 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 54641
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AVS AND 1TN4

1avs

1tn4


Resolution: 2.15→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 405 5 %random
Rwork0.2133 ---
all0.216 8045 --
obs0.216 7829 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.193 Å20 Å20 Å2
2--1.097 Å20 Å2
3---1.097 Å2
Refinement stepCycle: LAST / Resolution: 2.15→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 84 123 1388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.45
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.356 34 4 %
Rwork0.255 846 -
all-34 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4BEPRIDIL.PAR2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.356 / % reflection Rfree: 4 % / Rfactor Rwork: 0.255

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