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- PDB-4hrf: Atomic structure of DUSP26 -

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Basic information

Entry
Database: PDB / ID: 4hrf
TitleAtomic structure of DUSP26
ComponentsDual specificity protein phosphatase 26
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / Dual Specificity Phosphatase / p53 / nucleus
Function / homology
Function and homology information


MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / p53 binding / RNA polymerase II-specific DNA-binding transcription factor binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / 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 / Dual specificity protein phosphatase domain profile. / 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 / Dual specificity protein phosphatase domain profile. / 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 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLokareddy, R.K. / Bhardwaj, A. / Cingolani, G.
CitationJournal: Biochemistry / Year: 2013
Title: Atomic structure of dual-specificity phosphatase 26, a novel p53 phosphatase.
Authors: Lokareddy, R.K. / Bhardwaj, A. / Cingolani, G.
History
DepositionOct 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 26
B: Dual specificity protein phosphatase 26
C: Dual specificity protein phosphatase 26
D: Dual specificity protein phosphatase 26


Theoretical massNumber of molelcules
Total (without water)72,9524
Polymers72,9524
Non-polymers00
Water8,845491
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity protein phosphatase 26
C: Dual specificity protein phosphatase 26


Theoretical massNumber of molelcules
Total (without water)36,4762
Polymers36,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-26 kcal/mol
Surface area15840 Å2
MethodPISA
3
B: Dual specificity protein phosphatase 26
D: Dual specificity protein phosphatase 26


Theoretical massNumber of molelcules
Total (without water)36,4762
Polymers36,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.972, 82.260, 91.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA60 - 2121 - 153
21LEULEUBB60 - 2121 - 153
12ALAALAAA60 - 2111 - 152
22ALAALACC60 - 2111 - 152
13GLYGLYAA60 - 2081 - 149
23GLYGLYDD60 - 2081 - 149
14ALAALABB60 - 2111 - 152
24ALAALACC60 - 2111 - 152
15GLYGLYBB60 - 2081 - 149
25GLYGLYDD60 - 2081 - 149
16GLYGLYCC60 - 2081 - 149
26GLYGLYDD60 - 2081 - 149

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Dual specificity protein phosphatase 26 / Dual specificity phosphatase SKRP3 / Low-molecular-mass dual-specificity phosphatase 4 / DSP-4 / ...Dual specificity phosphatase SKRP3 / Low-molecular-mass dual-specificity phosphatase 4 / DSP-4 / LDP-4 / Mitogen-activated protein kinase phosphatase 8 / MAP kinase phosphatase 8 / MKP-8 / Novel amplified gene in thyroid anaplastic cancer


Mass: 18237.900 Da / Num. of mol.: 4 / Mutation: C152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP24, DUSP26, LDP4, MKP8, NATA1, SKRP3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BV47, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.15M Calcium Acetate, 0.1M Na Cacodylate pH 6.5, 17% PEG 8,000, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.97
SYNCHROTRONNSLS X26C21.075
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDJun 20, 2012
ADSC QUANTUM 315r2CCDJul 31, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.0751
ReflectionResolution: 1.68→15 Å / Num. all: 55848 / Num. obs: 55848 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.86 Å / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-2000data reduction
HKL-2000data scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→10 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.051 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21569 3450 5.1 %RANDOM
Rwork0.18505 ---
obs0.18659 -96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.144 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å2-0 Å2
2---0.68 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.68→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 0 491 5355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194983
X-RAY DIFFRACTIONr_bond_other_d0.0010.024882
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.9476733
X-RAY DIFFRACTIONr_angle_other_deg0.58311113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6475608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6121.529242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04115849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4351560
X-RAY DIFFRACTIONr_chiral_restr0.0520.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr9.39239865
X-RAY DIFFRACTIONr_sphericity_free26.108576
X-RAY DIFFRACTIONr_sphericity_bonded23.528510212
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90550.12
12B90550.12
21A81400.19
22C81400.19
31A83330.16
32D83330.16
41B81820.18
42C81820.18
51B84180.16
52D84180.16
61C80640.17
62D80640.17
LS refinement shellResolution: 1.683→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 260 -
Rwork0.309 4666 -
obs--98.34 %

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