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- PDB-2yub: Solution structure of the PDZ domain from mouse LIM domain kinase -

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Basic information

Entry
Database: PDB / ID: 2yub
TitleSolution structure of the PDZ domain from mouse LIM domain kinase
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / PDZ domain / LIMK-2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cornea development in camera-type eye / head development / astral microtubule organization / cis-Golgi network / mitotic spindle / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation ...cornea development in camera-type eye / head development / astral microtubule organization / cis-Golgi network / mitotic spindle / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHayashi, F. / Suetake, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PDZ domain from mouse LIM domain kinase
Authors: Hayashi, F. / Suetake, T. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)12,7991
Polymers12,7991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein LIM domain kinase 2 / LIMK-2


Mass: 12799.146 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: Limk2 / Plasmid: P041220-03
References: UniProt: O54785, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.47mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
CYANA2.1Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1438 restraints, 1347 are NOE-derived distance constraints, 91 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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