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- PDB-4y2e: Crystal structure of the catalytic domain of human dual-specifici... -

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Basic information

Entry
Database: PDB / ID: 4y2e
TitleCrystal structure of the catalytic domain of human dual-specificity phosphatase 7 (C232S)
ComponentsDual specificity protein phosphatase 7
KeywordsHYDROLASE / dual specificity phosphatase
Function / homology
Function and homology information


protein tyrosine phosphatase activity, metal-dependent / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / histone H2AXY142 phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / calmodulin-dependent protein phosphatase activity ...protein tyrosine phosphatase activity, metal-dependent / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / histone H2AXY142 phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / calmodulin-dependent protein phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / ERKs are inactivated / protein-serine/threonine phosphatase / negative regulation of MAP kinase activity / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / MAPK cascade / signal transduction / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dual specificity protein phosphatase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsLountos, G.T. / Austin, B.P. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of human dual-specificity phosphatase 7, a potential cancer drug target.
Authors: Lountos, G.T. / Austin, B.P. / Tropea, J.E. / Waugh, D.S.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 7
B: Dual specificity protein phosphatase 7
C: Dual specificity protein phosphatase 7
D: Dual specificity protein phosphatase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4258
Polymers67,0454
Non-polymers3804
Water13,403744
1
A: Dual specificity protein phosphatase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8562
Polymers16,7611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein phosphatase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8562
Polymers16,7611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dual specificity protein phosphatase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8562
Polymers16,7611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dual specificity protein phosphatase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8562
Polymers16,7611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.549, 64.458, 74.333
Angle α, β, γ (deg.)90.00, 91.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dual specificity protein phosphatase 7 / Dual specificity protein phosphatase PYST2


Mass: 16761.184 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 240-388) / Mutation: C232S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP7, PYST2 / Plasmid: pBA2529 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16829, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.3 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes,MOPS pH 7.5, 0.009 nitrate-sulfate-phosphate mixture, 37.5% v/v MPD-PEG1000-PEG3350; Morpheus Crystallization screen #32
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 70511 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 14
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LJ8

3lj8


Resolution: 1.67→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.844 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 3560 5.1 %RANDOM
Rwork0.15533 ---
obs0.15702 66922 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 20 744 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224988
X-RAY DIFFRACTIONr_bond_other_d0.0010.023332
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9676812
X-RAY DIFFRACTIONr_angle_other_deg0.90838193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36124.654217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4215851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6681516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.53069
X-RAY DIFFRACTIONr_mcbond_other0.1961.51224
X-RAY DIFFRACTIONr_mcangle_it1.30825012
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.05831919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2964.51800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.672→1.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 266 -
Rwork0.244 4806 -
obs--98.24 %

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