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- PDB-1koa: TWITCHIN KINASE FRAGMENT (C.ELEGANS), AUTOREGULATED PROTEIN KINAS... -

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Basic information

Entry
Database: PDB / ID: 1koa
TitleTWITCHIN KINASE FRAGMENT (C.ELEGANS), AUTOREGULATED PROTEIN KINASE AND IMMUNOGLOBULIN DOMAINS
ComponentsTWITCHIN
KeywordsKINASE / TWITCHIN / INTRASTERIC REGULATION
Function / homology
Function and homology information


positive regulation of sarcomere organization / positive regulation of locomotion / positive regulation of striated muscle contraction / A band / negative regulation of cell division / behavioral response to nicotine / M band / sarcomere organization / adult locomotory behavior / calmodulin binding ...positive regulation of sarcomere organization / positive regulation of locomotion / positive regulation of striated muscle contraction / A band / negative regulation of cell division / behavioral response to nicotine / M band / sarcomere organization / adult locomotory behavior / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / ATP binding / metal ion binding
Similarity search - Function
: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsKobe, B. / Heierhorst, J. / Feil, S.C. / Parker, M.W. / Benian, G.M. / Weiss, K.R. / Kemp, B.E.
Citation
Journal: EMBO J. / Year: 1996
Title: Giant protein kinases: domain interactions and structural basis of autoregulation.
Authors: Kobe, B. / Heierhorst, J. / Feil, S.C. / Parker, M.W. / Benian, G.M. / Weiss, K.R. / Kemp, B.E.
#1: Journal: Nature / Year: 1996
Title: Ca2+/S100 Regulation of Giant Protein Kinases
Authors: Heierhorst, J. / Kobe, B. / Feil, S.C. / Parker, M.W. / Benian, G.M. / Weiss, K.R. / Kemp, B.E.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TWITCHIN


Theoretical massNumber of molelcules
Total (without water)56,4261
Polymers56,4261
Non-polymers00
Water00
1
A: TWITCHIN

A: TWITCHIN


Theoretical massNumber of molelcules
Total (without water)112,8532
Polymers112,8532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_557-x+1/2,y,-z+21
Unit cell
Length a, b, c (Å)195.500, 195.500, 195.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein TWITCHIN


Mass: 56426.305 Da / Num. of mol.: 1 / Fragment: KINASE FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q23551

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.71 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris1reservoir
3200 mM1reservoirNaCl
42 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 17405 / % possible obs: 83.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.157
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.7 Å / Num. measured all: 39131

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 3.3→40 Å / σ(F): 0
Details: B-FACTORS WERE REFINED AS 2 GROUPS PER RESIDUE (MAIN-CHAIN ATOMS, SIDE-CHAIN ATOMS).
RfactorNum. reflection% reflection
Rfree0.351 -10 %
Rwork0.251 --
obs0.251 17405 -
Displacement parametersBiso mean: 88.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.55 Å
Luzzati sigma a-0.89 Å
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 0 0 3617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3425 / Rfactor Rwork: 0.2719
Solvent computation
*PLUS
Displacement parameters
*PLUS

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