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- PDB-1m0v: NMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH C... -

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Basic information

Entry
Database: PDB / ID: 1m0v
TitleNMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH COMPLEXED WITH THE SKAP-HOM PHOSPHO-PEPTIDE N-acetyl-DEpYDDPF-NH2
Components
  • PROTEIN-TYROSINE PHOSPHATASE YOPH
  • SKAP55 homologue
KeywordsHYDROLASE / high resolution structure
Function / homology
Function and homology information


Signal regulatory protein family interactions / B cell activation / : / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of cell population proliferation / extracellular region / nucleoplasm / plasma membrane ...Signal regulatory protein family interactions / B cell activation / : / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of cell population proliferation / extracellular region / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / SKAP family / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / SKAP family / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / PH domain / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Tyrosine-protein phosphatase YopH / Src kinase-associated phosphoprotein 2
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKhandelwal, P. / Keliikuli, K. / Smith, C.L. / Saper, M.A. / Zuiderweg, E.R.P.
Citation
Journal: Biochemistry / Year: 2002
Title: Solution structure and phosphopeptide binding to the N-terminal domain of Yersinia YopH: comparison with a crystal structure
Authors: Khandelwal, P. / Keliikuli, K. / Smith, C.L. / Saper, M.A. / Zuiderweg, E.R.P.
#1: Journal: MOL.MICROBIOL. / Year: 2001
Title: STRUCTURE OF THE TYPE III SECRETION AND SUBSTRATE-BINDING DOMAIN OF YERSINIA YOPH PHOSPHATASE
Authors: SMITH, C.L. / KHANDELWAL, P. / KELIIKULI, K. / ZUIDERWEG, E.R.P. / SAPER, M.A.
#2: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 15N AND 13C ASSIGNMENTS OF THE N-TERMINAL DOMAIN OF YERSINIA OUTER PROTEIN H IN ITS APO FORM AND IN COMPLEX WITH A PHOSPHOTYROSINE PEPTIDE
Authors: KHANDELWAL, P. / KELIIKULI, K. / SMITH, C.L. / SAPER, M.A. / ZUIDERWEG, E.R.P.
History
DepositionJun 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE YOPH
B: SKAP55 homologue


Theoretical massNumber of molelcules
Total (without water)15,8862
Polymers15,8862
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 / 360structures with the least restraint violations
RepresentativeModel #9best ramachandran plot

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE YOPH / VIRULENCE PROTEIN


Mass: 14882.599 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL DOMAIN (RESIDUES 1-129)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: p08538, UniProt: P08538*PLUS, protein-tyrosine-phosphatase
#2: Protein/peptide SKAP55 homologue / SKAP-HOM PEPTIDE


Mass: 1003.879 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS peptide WAS CHEMICALLY synthesiZED. It is naturally found in Mus musculus (mouse).
References: GenBank: 13277602, UniProt: Q3UND0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-resolved NOESY
1213D 15N-resolved NOESY
1313D (H)CCH
1413D 15N/13C filtered/edited NOESY
NMR detailsText: 15N HSQC titrations

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Sample preparation

DetailsContents: 0.6 mM YopHNT U-15N,13C complexed with 0.72 mM unlabeled peptide; 50mM phosphate buffer NA
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mm phosphate / pH: 6.5 / Pressure: ambient / Temperature: 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
Varian INOVAVarianINOVA8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeprocessing
XEASYdata analysis
CNSstructure solution
ARIA1Nilges, M. and O'Donoghue, S.I.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 3472 restraints, 3222 are NOE-derived distance constraints, 152 dihedral angle restraints, 98 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: best ramachandran plot
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 360 / Conformers submitted total number: 20

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