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- PDB-1j4x: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE C124S MUTANT-PEPTI... -

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Basic information

Entry
Database: PDB / ID: 1j4x
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE C124S MUTANT-PEPTIDE COMPLEX
Components
  • DDE(AHP)(TPO)G(PTR)VATR
  • DUAL SPECIFICITY PROTEIN PHOSPHATASE 3
KeywordsHYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE
Function / homology
Function and homology information


peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / ERKs are inactivated / negative regulation of JNK cascade / motile cilium / regulation of focal adhesion assembly ...peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / ERKs are inactivated / negative regulation of JNK cascade / motile cilium / regulation of focal adhesion assembly / dephosphorylation / negative regulation of T cell receptor signaling pathway / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / phosphatase activity / peptidyl-tyrosine dephosphorylation / immunological synapse / negative regulation of MAPK cascade / cytoskeletal protein binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of mitotic cell cycle / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytoskeleton / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.75 Å
AuthorsSchumacher, M.A. / Todd, J.L. / Tanner, K.G. / Denu, J.M.
CitationJournal: Biochemistry / Year: 2002
Title: Structural basis for the recognition of a bisphosphorylated MAP kinase peptide by human VHR protein Phosphatase.
Authors: Schumacher, M.A. / Todd, J.L. / Rice, A.E. / Tanner, K.G. / Denu, J.M.
History
DepositionDec 13, 2001Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 19, 2001ID: 1F5D
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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 PROTEIN PHOSPHATASE 3
D: DDE(AHP)(TPO)G(PTR)VATR


Theoretical massNumber of molelcules
Total (without water)21,7682
Polymers21,7682
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-10 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.390, 55.770, 101.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DUAL SPECIFICITY PROTEIN PHOSPHATASE 3


Mass: 20354.012 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7-7-VHR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51452, protein-tyrosine-phosphatase
#2: Protein/peptide DDE(AHP)(TPO)G(PTR)VATR


Mass: 1414.283 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, ISOPROPANOL, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-15 mg/mlprotein1drop
220 %PEG40001reservoir
310 %2-propanol1reservoir
40.1 Mcitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 9234 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.1
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.29 / % possible all: 80
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 10 Å / Num. measured all: 16753

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Processing

Software
NameVersionClassification
MERLOTphasing
TNTrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 2.75→10 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.26 810 8.96 %RANDOM
Rwork0.188 ---
all0.192 16753 --
obs0.192 9236 90 %-
Refinement stepCycle: LAST / Resolution: 2.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 0 66 1546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.78
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.192 / Rfactor obs: 0.188 / Rfactor Rfree: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS

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