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- PDB-1vhr: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1vhr
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE
ComponentsHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
KeywordsHYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE
Function / homology
Function and homology information


receptor signaling protein tyrosine kinase inhibitor 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 / dephosphorylation / negative regulation of JNK cascade / regulation of focal adhesion assembly ...receptor signaling protein tyrosine kinase inhibitor 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 / dephosphorylation / negative regulation of JNK cascade / regulation of focal adhesion assembly / motile cilium / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / protein serine/threonine phosphatase activity / phosphatase activity / peptidyl-tyrosine dephosphorylation / immunological synapse / cytoskeletal protein binding / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / cytoskeleton / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / 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 / MIR SOFTWARE USED : PHASES STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 2.1 Å
AuthorsYuvaniyama, J. / Denu, J.M. / Dixon, J.E. / Saper, M.A.
Citation
Journal: Science / Year: 1996
Title: Crystal structure of the dual specificity protein phosphatase VHR.
Authors: Yuvaniyama, J. / Denu, J.M. / Dixon, J.E. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: The Purification and Characterization of a Human Dual-Specific Protein Tyrosine Phosphatase
Authors: Denu, J.M. / Zhou, G. / Wu, L. / Zhao, R. / Yuvaniyama, J. / Saper, M.A. / Dixon, J.E.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: The Catalytic Role of Cys124 in the Dual Specificity Phosphatase Vhr
Authors: Zhou, G. / Denu, J.M. / Wu, L. / Dixon, J.E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Expression Cloning of a Human Dual-Specificity Phosphatase
Authors: Ishibashi, T. / Bottaro, D.P. / Chan, A. / Miki, T. / Aaronson, S.A.
History
DepositionFeb 20, 1996Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
B: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0754
Polymers40,7402
Non-polymers3342
Water2,540141
1
A: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6082
Polymers20,3701
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4662
Polymers20,3701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.148, 60.040, 52.016
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.962481, -0.060958, -0.264412), (-0.050633, 0.997671, -0.045694), (0.266582, -0.030591, -0.963327)
Vector: 28.16632, 29.73183, 25.95833)

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Components

#1: Protein HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR / VHR


Mass: 20370.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: ORIGINAL GENE GDB\:DUSP3; VHR, CHROMOSOME MAP POSITION 17Q21
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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: THE FULL-LENGTH VHR (RESIDUES 2 - 185) WAS CRYSTALLIZED AT A CONCENTRATION OF 5-6 MG/ML WITH 14% POLYETHYLENE GLYCOL 4000, 22.5 MM LITHIUM SULFATE, 50 MM HEPES PH 7.0, AND 0.05% BETA- ...Details: THE FULL-LENGTH VHR (RESIDUES 2 - 185) WAS CRYSTALLIZED AT A CONCENTRATION OF 5-6 MG/ML WITH 14% POLYETHYLENE GLYCOL 4000, 22.5 MM LITHIUM SULFATE, 50 MM HEPES PH 7.0, AND 0.05% BETA-MERCAPTOETHANOL IN A HANGING DROP OF 20 MICROLITERS. THE DROP WAS EQUILIBRATED AGAINST 1 ML OF TWICE THE CONCENTRATION OF PRECIPITANT SOLUTION AT 23 DEGREE CELSIUS., vapor diffusion - hanging drop, temperature 296K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlVHR1drop
210-15 %PEG40001drop
322 mM1dropLi2SO4
40.1 %beta-mercaptoethanol1drop
550 mMHEPES1drop
6precipitant1reservoirtwice the concentration

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 27, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→90 Å / Num. obs: 18952 / % possible obs: 86.4 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. measured all: 41078

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR SOFTWARE USED : PHASES STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.254 -9.96 %
Rwork0.176 --
obs0.176 18746 86.4 %
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 20 141 2929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.654
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.87
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.87

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