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- PDB-1tki: AUTOINHIBITED SERINE KINASE DOMAIN OF THE GIANT MUSCLE PROTEIN TITIN -

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Basic information

Entry
Database: PDB / ID: 1tki
TitleAUTOINHIBITED SERINE KINASE DOMAIN OF THE GIANT MUSCLE PROTEIN TITIN
ComponentsTITIN
KeywordsSERINE KINASE / TITIN / MUSCLE / AUTOINHIBITION
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation / cardiac muscle hypertrophy / cardiac muscle tissue morphogenesis / actinin binding / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, SINGLE CRYSTAL AVERAGING / Resolution: 2 Å
AuthorsMayans, M.O. / Gautel, M. / Wilmanns, M.
Citation
Journal: Nature / Year: 1998
Title: Structural basis for activation of the titin kinase domain during myofibrillogenesis.
Authors: Mayans, O. / van der Ven, P.F. / Wilm, M. / Mues, A. / Young, P. / Furst, D.O. / Wilmanns, M. / Gautel, M.
#1: Journal: To be Published
Title: X-Ray Analysis of Protein Crystals with Thin Plate Morphology
Authors: Mayans, O. / Wilmanns, M.
History
DepositionMay 29, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_distant_solvent_atoms ...diffrn_source / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 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: TITIN
B: TITIN


Theoretical massNumber of molelcules
Total (without water)74,3382
Polymers74,3382
Non-polymers00
Water9,260514
1
A: TITIN


Theoretical massNumber of molelcules
Total (without water)37,1691
Polymers37,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TITIN


Theoretical massNumber of molelcules
Total (without water)37,1691
Polymers37,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.610, 89.770, 113.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999999, 0.00086, -0.001243), (0.000845, 0.999922, 0.012453), (0.001254, 0.012452, -0.999922)
Vector: 78.6986, -1.6236, 133.3774)

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Components

#1: Protein TITIN


Mass: 37168.898 Da / Num. of mol.: 2 / Fragment: KINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Organ: HEART / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q10466, UniProt: Q8WZ42*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.63 Å3/Da / Density % sol: 47 %
Crystal grow
*PLUS
pH: 4.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.1 Msodium/potassium tartrate1reservoir
22.5 %(v/v)ethanol1reservoir
325 mMsodium acetate1reservoir
425 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: PREMIRROR/BENT MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 53151 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.077
Reflection shellResolution: 2→2.39 Å / Redundancy: 2.6 % / Rsym value: 0.239 / % possible all: 94.45
Reflection
*PLUS
Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement, SINGLE CRYSTAL AVERAGING
Starting model: TRIMMED VERSION OF THE CATALYTIC DOMAIN OF TWITCHIN KINASE (1KOB)

1kob


Resolution: 2→40 Å / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -5 %RANDOM
Rwork0.207 ---
obs0.207 53151 96 %-
Displacement parametersBiso mean: 22.09 Å2
Baniso -1Baniso -2Baniso -3
1-6.23 Å20 Å20 Å2
2---6.21 Å20 Å2
3----0.018 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 0 514 5738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.296
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.98
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.082
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINED / Weight Biso : 1 / Weight position: 300
LS refinement shellResolution: 2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.274 -5 %
Rwork0.224 15787 -
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.98
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.082
LS refinement shell
*PLUS
Rfactor obs: 0.224

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