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- PDB-2fek: Structure of a protein tyrosine phosphatase -

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Basic information

Entry
Database: PDB / ID: 2fek
TitleStructure of a protein tyrosine phosphatase
ComponentsLow molecular weight protein-tyrosine-phosphatase wzb
KeywordsHYDROLASE / LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE / ESCHERICHIA COLI / PHOSPHATE BINDING
Function / homology
Function and homology information


colanic acid biosynthetic process / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Low molecular weight protein-tyrosine-phosphatase Wzb
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodSOLUTION NMR / 200 structures were generated in CYANA. The 100 structures with lowest energy were further refined in AMBER7. The 20 lowest energy structures were finally selected.
AuthorsLescop, E. / Jin, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The solution structure of Escherichia coli Wzb reveals a novel substrate recognition mechanism of prokaryotic low molecular weight protein-tyrosine phosphatases
Authors: Lescop, E. / Hu, Y. / Xu, H. / Hu, W. / Chen, J. / Xia, B. / Jin, C.
History
DepositionDec 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Low molecular weight protein-tyrosine-phosphatase wzb


Theoretical massNumber of molelcules
Total (without water)18,9051
Polymers18,9051
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Low molecular weight protein-tyrosine-phosphatase wzb


Mass: 18904.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: wzb / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AAB2, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
NMR detailsText: 97 1H-15N residual dipolar, measured in PEG/hexanol (5.5 wt%, molar ratio=0.92), were included in structure calculation.

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1mM WZB U-15N, 13C; 50mM sodium phosphate, 50mM NaCl buffer; 25mM DTT; 5mM EDTA; pH 690% H2O/10% D2O
2~1mM WZB U-15N; 50mM sodium phosphate, 50mM NaCl buffer; 25mM DTT; 5mM EDTA; pH 690% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe1Delaglioprocessing
CYANA1.2Guentertstructure solution
Amber7Caserefinement
NMRView5Blevinsdata analysis
RefinementMethod: 200 structures were generated in CYANA. The 100 structures with lowest energy were further refined in AMBER7. The 20 lowest energy structures were finally selected.
Software ordinal: 1
Details: A total of 4689 restraints were used. Included are 1630 ambiguous and 2640 unambiguous NOE-derived distances, 100 hydrogen bond restraints, 190 backbone dihedral angles, 32 side-chain chi1 ...Details: A total of 4689 restraints were used. Included are 1630 ambiguous and 2640 unambiguous NOE-derived distances, 100 hydrogen bond restraints, 190 backbone dihedral angles, 32 side-chain chi1 and 97 1H-15N residual dipolar couplings values.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

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