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Basic information

Entry
Database: PDB / ID: 5xjv
TitleTwo intermediate states of conformation switch in dual specificity phosphatase 13a
ComponentsDual specificity protein phosphatase 13 isoform A
KeywordsHYDROLASE / DUSP13A / PTP / conformation switch / Catalytic Domain
Function / homology
Function and homology information


myosin phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-serine/threonine phosphatase / phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / 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 / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...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 / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / 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
PHOSPHATE ION / Dual specificity protein phosphatase 13A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWei, C.H. / Min, H.G. / Chun, H.J. / Ryu, S.E.
CitationJournal: Pharmacol. Res. / Year: 2018
Title: Two intermediate states of the conformational switch in dual specificity phosphatase 13a
Authors: Wei, C.H. / Min, H.G. / Kim, M. / Kim, G.H. / Chun, H.J. / Ryu, S.E.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 13 isoform A
B: Dual specificity protein phosphatase 13 isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7224
Polymers40,5322
Non-polymers1902
Water7,458414
1
A: Dual specificity protein phosphatase 13 isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3612
Polymers20,2661
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-8 kcal/mol
Surface area8460 Å2
MethodPISA
2
B: Dual specificity protein phosphatase 13 isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3612
Polymers20,2661
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-8 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.037, 89.343, 45.897
Angle α, β, γ (deg.)90.00, 89.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dual specificity protein phosphatase 13 isoform A / DUSP13A / Branching-enzyme interacting DSP / Muscle-restricted DSP / MDSP


Mass: 20266.023 Da / Num. of mol.: 2 / Fragment: UNP residues 1-185 / Mutation: C18A, C35A, C77A, C129S, C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP13, BEDP, DUSP13A, MDSP / Production host: Escherichia coli (E. coli)
References: UniProt: Q6B8I1, 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.: 414 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl (pH 8.5), 20% ethanol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 35981 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 31.5
Reflection shellResolution: 1.69→1.72 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
MOLREPphasing
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GWO

2gwo


Resolution: 1.69→45.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.213 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22057 1826 5.1 %RANDOM
Rwork0.17786 ---
obs0.18015 34155 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20.19 Å2
2--2.44 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.69→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 10 414 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192733
X-RAY DIFFRACTIONr_bond_other_d0.0010.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9443721
X-RAY DIFFRACTIONr_angle_other_deg1.02535831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73522.258124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36215418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3561524
X-RAY DIFFRACTIONr_chiral_restr0.1320.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213065
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02607
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_it2.5471.8311362
X-RAY DIFFRACTIONr_mcbond_other2.5291.8281361
X-RAY DIFFRACTIONr_mcangle_it3.7372.7351699
X-RAY DIFFRACTIONr_mcangle_other3.7362.7371700
X-RAY DIFFRACTIONr_scbond_it2.8352.0761371
X-RAY DIFFRACTIONr_scbond_other2.8322.0811364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2693.0012011
X-RAY DIFFRACTIONr_long_range_B_refined6.77823.6913227
X-RAY DIFFRACTIONr_long_range_B_other6.62722.7333099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.687→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 108 -
Rwork0.219 2364 -
obs--93.28 %

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