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- PDB-2mbc: Solution Structure of human holo-PRL-3 in complex with vanadate -

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Basic information

Entry
Database: PDB / ID: 2mbc
TitleSolution Structure of human holo-PRL-3 in complex with vanadate
ComponentsProtein tyrosine phosphatase type IVA 3
KeywordsHYDROLASE / holo-PRL-3 / vanadate
Function / homology
Function and homology information


regulation of vascular endothelial growth factor signaling pathway / : / positive regulation of establishment of protein localization / positive regulation of vascular permeability / endothelial cell migration / Notch signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cellular response to leukemia inhibitory factor / positive regulation of non-canonical NF-kappaB signal transduction ...regulation of vascular endothelial growth factor signaling pathway / : / positive regulation of establishment of protein localization / positive regulation of vascular permeability / endothelial cell migration / Notch signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cellular response to leukemia inhibitory factor / positive regulation of non-canonical NF-kappaB signal transduction / early endosome / regulation of DNA-templated transcription / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain ...: / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsJeong, K. / Kang, D. / Kim, J. / Shin, S. / Jin, B. / Lee, C. / Kim, E. / Jeon, Y.H. / Kim, Y.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and backbone dynamics of vanadate-bound PRL-3: comparison of 15N nuclear magnetic resonance relaxation profiles of free and vanadate-bound PRL-3.
Authors: Jeong, K.W. / Kang, D.I. / Lee, E. / Shin, A. / Jin, B. / Park, Y.G. / Lee, C.K. / Kim, E.H. / Jeon, Y.H. / Kim, E.E. / Kim, Y.
History
DepositionJul 29, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase type IVA 3


Theoretical massNumber of molelcules
Total (without water)18,2681
Polymers18,2681
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein tyrosine phosphatase type IVA 3 / PRL-R / Protein-tyrosine phosphatase 4a3 / Protein-tyrosine phosphatase of regenerating liver 3 / PRL-3


Mass: 18268.291 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A3, PRL3 / Production host: Escherichia coli (E. coli) / References: UniProt: O75365, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCA
1413D HN(CO)CA
1513D HNHA
1613D (H)CCH-TOCSY
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 50mM HEPES-1, 100mM NaCl-2, 10mM DTT-3, 3mM sodium orthovanadate-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMHEPES-11
100 mMNaCl-21
10 mMDTT-31
3 mMsodium orthovanadate-41
Sample conditionspH: 7.3 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANASchwieters, Kuszewski, Tjandra and Clorerefinement
CYANASchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
CYANAGoddardstructure solution
XPLOR_NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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