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- PDB-2ai6: Solution structure of human phosphohistidine phosphatase 1 -

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Basic information

Entry
Database: PDB / ID: 2ai6
TitleSolution structure of human phosphohistidine phosphatase 1
Components14 kDa phosphohistidine phosphatase
KeywordsHYDROLASE / alpha/beta architecture
Function / homology
Function and homology information


phosphohistidine phosphatase / peptidyl-histidine dephosphorylation / negative regulation of lyase activity / negative regulation of ATP citrate synthase activity / protein histidine phosphatase activity / lamellipodium organization / leading edge of lamellipodium / positive regulation of cell motility / negative regulation of T cell receptor signaling pathway / calcium channel inhibitor activity ...phosphohistidine phosphatase / peptidyl-histidine dephosphorylation / negative regulation of lyase activity / negative regulation of ATP citrate synthase activity / protein histidine phosphatase activity / lamellipodium organization / leading edge of lamellipodium / positive regulation of cell motility / negative regulation of T cell receptor signaling pathway / calcium channel inhibitor activity / protein dephosphorylation / actin filament binding / actin cytoskeleton organization / transmembrane transporter binding / nuclear body / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Janus/Ocnus / Janus / Janus superfamily / Janus/Ocnus family (Ocnus) / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
14 kDa phosphohistidine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsGong, W. / Cui, G. / Jin, C. / Xia, B.
CitationJournal: Biochem.J. / Year: 2009
Title: Solution structure and catalytic mechanism of human protein histidine phosphatase 1.
Authors: Gong, W. / Li, Y. / Cui, G. / Hu, J. / Fang, H. / Jin, C. / Xia, B.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14 kDa phosphohistidine phosphatase


Theoretical massNumber of molelcules
Total (without water)13,8521
Polymers13,8521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 14 kDa phosphohistidine phosphatase / Phosphohistidine phosphatase 1 / Protein janus-A homolog


Mass: 13851.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q9NRX4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB,CBCA(CO)NH
121HNCO,HN(CA)CO
131HC(C)H COSY
141HC(C)H TOCSY
1513D 13C-separated NOESY
1613D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM PHPT1, 50mM PBS, 50mM NaCl, 30mM DTT; 90%H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipecyana 2.0F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
NMRView5B. A. Johnson and R. A. Blevinsdata analysis
DYANAcyana2.0Guntert, P., Mumenthaler, C. & W thrich, Kstructure solution
Amber7David A. Case, et. al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: torsion angle dynamics performed by DYANA, simulated annealing performed by AMBER
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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