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- PDB-1kob: TWITCHIN KINASE FRAGMENT (APLYSIA), AUTOREGULATED PROTEIN KINASE ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1kob
TitleTWITCHIN KINASE FRAGMENT (APLYSIA), AUTOREGULATED PROTEIN KINASE DOMAIN
ComponentsTWITCHIN
KeywordsKINASE / TWITCHIN / INTRASTERIC REGULATION
Function / homology
Function and homology information


intracellular signal transduction / positive regulation of apoptotic process / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Immunoglobulin I-set / Immunoglobulin I-set domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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
VALINE / Twitchin-like protein
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: TWITCHIN
B: TWITCHIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5813
Polymers89,4642
Non-polymers1171
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-14 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.300, 87.800, 152.900
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 TWITCHIN


Mass: 44731.879 Da / Num. of mol.: 2 / Fragment: KINASE FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Gene: CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: Q16980
#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.4 mg/mlprotein1drop
315 %PEG40001reservoir
4100 mMsodium citrate1reservoir
51 mMdithiothreitol1reservoir
2PEG40001drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33532 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.118
Reflection
*PLUS
Num. measured all: 153335

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.3→40 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.282 -10 %
Rwork0.1999 --
obs0.1999 33532 -
Displacement parametersBiso mean: 31.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5746 0 0 326 6072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.677
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5

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