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- PDB-5y15: Crystal structure of human DUSP28 -

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Basic information

Entry
Database: PDB / ID: 5y15
TitleCrystal structure of human DUSP28
ComponentsDual specificity phosphatase 28
KeywordsHYDROLASE / DUSP28 / dual-specificity phosphatase / DUSP / protein tyrosine phosphatase / PTP
Function / homology
Function and homology information


dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
: / 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 domain / Tyrosine specific protein phosphatases domain profile. ...: / 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dual specificity phosphatase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKu, B. / Hong, W. / Kim, S.J. / Ryu, S.E.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation of Korea2015M3A9B5030308 Korea, Republic Of
National Research Foundation of Korea2015M3A9B5029741 Korea, Republic Of
Korea Research Institute of Bioscience and BiotechnologyResearch Initiative Program Korea, Republic Of
CitationJournal: PLoS ONE / Year: 2017
Title: Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28
Authors: Ku, B. / Hong, W. / Keum, C.W. / Kim, M. / Ryu, H. / Jeon, D. / Shin, H.C. / Kim, J.H. / Kim, S.J. / Ryu, S.E.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity phosphatase 28
B: Dual specificity phosphatase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3934
Polymers41,2032
Non-polymers1902
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-24 kcal/mol
Surface area12460 Å2
Unit cell
Length a, b, c (Å)78.952, 78.952, 90.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dual specificity phosphatase 28


Mass: 20601.500 Da / Num. of mol.: 2 / Mutation: R59Q, C103S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4G0W2, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 300 mM NaCl, and 26% [w/v] polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19301 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 47.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.288 / Rsym value: 0.288 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HCM

2hcm


Resolution: 2.1→31.971 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 29.18
RfactorNum. reflection% reflection
Rfree0.2694 1944 10.07 %
Rwork0.2188 --
obs0.2239 19301 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→31.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 10 42 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012205
X-RAY DIFFRACTIONf_angle_d1.3612999
X-RAY DIFFRACTIONf_dihedral_angle_d14.7471359
X-RAY DIFFRACTIONf_chiral_restr0.06334
X-RAY DIFFRACTIONf_plane_restr0.008402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1004-2.1530.37961370.32461219X-RAY DIFFRACTION99
2.153-2.21120.32991330.29111216X-RAY DIFFRACTION99
2.2112-2.27620.33361380.2711223X-RAY DIFFRACTION99
2.2762-2.34970.29191350.25661212X-RAY DIFFRACTION100
2.3497-2.43360.28811370.24881228X-RAY DIFFRACTION100
2.4336-2.5310.30921400.24441237X-RAY DIFFRACTION99
2.531-2.64610.29731340.23321215X-RAY DIFFRACTION99
2.6461-2.78560.2861410.23181237X-RAY DIFFRACTION99
2.7856-2.960.2841360.2451225X-RAY DIFFRACTION100
2.96-3.18830.31251400.24281249X-RAY DIFFRACTION100
3.1883-3.50880.26841380.23121251X-RAY DIFFRACTION100
3.5088-4.01570.28041410.19921263X-RAY DIFFRACTION100
4.0157-5.05620.20191460.17531273X-RAY DIFFRACTION100
5.0562-31.97440.24891480.19811309X-RAY DIFFRACTION98

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