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- PDB-1mzk: NMR structure of kinase-interacting FHA domain of kinase associat... -

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Basic information

Entry
Database: PDB / ID: 1mzk
TitleNMR structure of kinase-interacting FHA domain of kinase associated protein phosphatase, KAPP in Arabidopsis
ComponentsKINASE ASSOCIATED PROTEIN PHOSPHATASE
KeywordsHYDROLASE / BETA SANDWICH
Function / homology
Function and homology information


[pyruvate kinase]-phosphatase activity / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Kinase associated protein phosphatase / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Tumour Suppressor Smad4 - #20 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...Kinase associated protein phosphatase / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Tumour Suppressor Smad4 - #20 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein phosphatase 2C 70
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing in cartesian space, residual dipolar couplings
AuthorsLee, G. / Ding, Z. / Walker, J.C. / Van Doren, S.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: NMR Structure of the forkhead-associated domain from the Arabidopsis receptor kinase-associated protein phosphatase.
Authors: Lee, G. / Ding, Z. / Walker, J.C. / Van Doren, S.R.
History
DepositionOct 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
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: KINASE ASSOCIATED PROTEIN PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)14,8861
Polymers14,8861
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)30 / 100structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein KINASE ASSOCIATED PROTEIN PHOSPHATASE


Mass: 14885.836 Da / Num. of mol.: 1 / Fragment: KINASE INTERACTION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: KAPP / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P46014, protein-serine/threonine phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HMQC-J
24215N HSQC for H/D exhange
3533D HNCO for 1Dnco, 1Dcaco
36315N HSQC for 1Dnh
47415N HSQC for 1Dnh
3833D HNCA for 1Dcaha
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Residues preceding 180 originated from linker of GST tag. Residues beyond 298 are unstructured. Note that in all the models ...Text: The structure was determined using triple-resonance NMR spectroscopy. Residues preceding 180 originated from linker of GST tag. Residues beyond 298 are unstructured. Note that in all the models the residues A175-A176 and A299-A313 are disordered and missing from the model

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM kinase interacting FHA domain; 20mM phosphate pH6.3; 120mM NaCl, 93% H2O, 7%D2O93% H2O/7% D2O
20.6mM kinase interacting FHA domain; 20mM phosphate pH6.3; 120mM NaCl, 100%D2O100% D2O
30.5mM kinase interacting FHA domain; 20mM phosphate pH6.3; 120mM NaCl, 9.5mg/ml Pf1 phage, 90%H2O, 10%D2O90% H2O/10% D2O
40.4mM kinase interacting FHA domain; 20mM phosphate pH6.3; 120mM NaCl, 5% C12H6/Hexanol,90%H2O, 10%D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM phosphaste/120mM NaCl 6.3 ambient 295 K
220mM phosphaste/120mM NaCl 6.3 ambient 293 K
320mM phosphaste/120mM NaCl 6.3 ambient 298 K
420mM phosphaste/120mM NaCl/5%PEG/hexano 6.3 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR1.3Brukercollection
VNMR6.1BVariancollection
SYBYL6.3Triposprocessing
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: torsion angle dynamics, simulated annealing in cartesian space, residual dipolar couplings
Software ordinal: 1
Details: the structures are based on 1313 interresidue NOE-derived distance constraints, 176 dihedral angle restraints, 54 distance restraints from hydrogen bonds,as well as 131 1Dnh, 55 1Dcaha, 37 ...Details: the structures are based on 1313 interresidue NOE-derived distance constraints, 176 dihedral angle restraints, 54 distance restraints from hydrogen bonds,as well as 131 1Dnh, 55 1Dcaha, 37 1Dnco, 58 1Dcaco residual dipolar coupling restraints. The covalent bond angle deviations, listed in remark 500, result from refinement using residual dipolar couplings and have occurred in some structures with high energy. The residues with torsion angle deviations are relatively mobile and poorly defined in the model.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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