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- PDB-1t3k: NMR structure of a CDC25-like dual-specificity tyrosine phosphata... -

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Basic information

Entry
Database: PDB / ID: 1t3k
TitleNMR structure of a CDC25-like dual-specificity tyrosine phosphatase of Arabidopsis thaliana
ComponentsDual-specificity tyrosine phosphatase
KeywordsHYDROLASE / CDC25 / cell cycle / phosphorylation / plant
Function / homology
Function and homology information


sequestering of metal ion / arsenate reductase (glutathione/glutaredoxin) / arsenate reductase (glutaredoxin) activity / response to arsenic-containing substance / protein-tyrosine-phosphatase / chloroplast / protein tyrosine phosphatase activity / protein phosphorylation / cell division / mitochondrion ...sequestering of metal ion / arsenate reductase (glutathione/glutaredoxin) / arsenate reductase (glutaredoxin) activity / response to arsenic-containing substance / protein-tyrosine-phosphatase / chloroplast / protein tyrosine phosphatase activity / protein phosphorylation / cell division / mitochondrion / nucleus / metal ion binding
Similarity search - Function
Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dual specificity phosphatase Cdc25
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsLandrieu, I. / da Costa, M. / De Veylder, L. / Dewitte, F. / Vandepoele, K. / Hassan, S. / Wieruszeski, J.M. / Faure, J.D. / Inze, D. / Lippens, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana.
Authors: Landrieu, I. / Da Costa, M. / De Veylder, L. / Dewitte, F. / Vandepoele, K. / Hassan, S. / Wieruszeski, J.M. / Faure, J.D. / Van Montagu, M. / Inze, D. / Lippens, G.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: Dual-specificity tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0072
Polymers16,9411
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Dual-specificity tyrosine phosphatase / Arath CDC25


Mass: 16941.219 Da / Num. of mol.: 1 / Mutation: C72S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDC25 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q8GY31, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CO
1213D HNCO
1313D CBCA(CO)NH
1413D HNCA
1523D 15N-separated NOESY
1633D 13C-separated NOESY
NMR detailsText: cryo-probehead

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 microM U-15N,13C Arath;CDC2525 mM phosphate buffer, pH7.6 250 mM NaCl 5 mM b-mercapthoethanol 95% H2O, 5% D2O
2400 microM U-15N Arath;CDC2525 mM phosphate buffer, pH7.6 250 mM NaCl 5 mM b-mercapthoethanol 95% H2O, 5% D2O
3400 microM 13C Arath;CDC2525 mM phosphate buffer, pH7.6 250 mM NaCl 5 mM b-mercapthoethanol 100%D2O
Sample conditionspH: 7.6 / Pressure: ambient / Temperature: 293 K

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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 DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
SNARFFrank Van Hoesel, Groningen, the Netherlandsprocessing
CNS1.1Brunger et al.structure solution
CNS1.1Brunger et al.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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