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- PDB-1avs: X-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMA... -

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Basic information

Entry
Database: PDB / ID: 1avs
TitleX-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMAIN OF TROPONIN C
ComponentsTROPONIN C
KeywordsMUSCLE CONTRACTION / CALCIUM-ACTIVATED / TROPONIN / E-F HAND CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


troponin complex / Striated Muscle Contraction / myosin II 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Troponin C, skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 1.75 Å
AuthorsStrynadka, N.C.J. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structural details of a calcium-induced molecular switch: X-ray crystallographic analysis of the calcium-saturated N-terminal domain of troponin C at 1.75 A resolution.
Authors: Strynadka, N.C. / Cherney, M. / Sielecki, A.R. / Li, M.X. / Smillie, L.B. / James, M.N.
History
DepositionSep 19, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_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_asym_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_asym_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROPONIN C
B: TROPONIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1286
Polymers19,9682
Non-polymers1604
Water1,67593
1
A: TROPONIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0643
Polymers9,9841
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TROPONIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0643
Polymers9,9841
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.120, 81.580, 39.860
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.694896, -0.010889, 0.719028), (-0.018211, -0.999831, 0.002459), (0.71888, -0.014803, -0.694977)
Vector: -18.851, 23.342, 43.775)

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Components

#1: Protein TROPONIN C


Mass: 9984.085 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1 - 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: BREAST / Production host: Escherichia coli (E. coli) / References: UniProt: P02588
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.4 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: 72 % AMMONIUM SULFATE 100 MM TRIS 2 % MPD, 5 MM CALCIUM CHLORIDE PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
272 %(w/v)ammonium sulfate1reservoir
3100 mMTris-HCl1reservoir
45 mM1reservoirCaCl2
52 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: NO MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 18010 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.104 / Net I/σ(I): 15
Reflection shellResolution: 1.75→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3 / Rsym value: 0.28 / % possible all: 82
Reflection
*PLUS
Num. measured all: 85689
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
AMoREphasing
MLPHAREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR
Starting model: PDB ENTRY 4TNC

4tnc


Resolution: 1.75→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.25 1801 10 %
Rwork0.214 --
all0.22 18010 -
obs0.22 18010 92 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 4 93 1360
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01613400.9
X-RAY DIFFRACTIONt_angle_deg2.917891.1
X-RAY DIFFRACTIONt_dihedral_angle_d18.468400
X-RAY DIFFRACTIONt_incorr_chiral_ct1
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015541.2
X-RAY DIFFRACTIONt_gen_planes0.0151873
X-RAY DIFFRACTIONt_it2.613400.3
X-RAY DIFFRACTIONt_nbd0.0384812
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.214 / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.460
X-RAY DIFFRACTIONt_plane_restr0.0153

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