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- PDB-2pq5: Crystal structure of Dual specificity protein phosphatase 13 (DUSP13) -

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Basic information

Entry
Database: PDB / ID: 2pq5
TitleCrystal structure of Dual specificity protein phosphatase 13 (DUSP13)
ComponentsDual specificity protein phosphatase 13
KeywordsHYDROLASE / Protein phosphatase / Dual specificity phosphatase / DUSP13 / Testis and skeletal muscle specific DSP / Structural Genomics / Structural Genomics Consortium / SGC
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 / phosphatase activity / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / meiotic cell cycle ...MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / meiotic cell cycle / protein tyrosine phosphatase activity / spermatogenesis / 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 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUgochukwu, E. / Salah, E. / Savitsky, P. / Barr, A. / Pantic, N. / Niesen, F. / Burgess-Brown, N. / Berridge, G. / Bunkoczi, G. / Uppenberg, J. ...Ugochukwu, E. / Salah, E. / Savitsky, P. / Barr, A. / Pantic, N. / Niesen, F. / Burgess-Brown, N. / Berridge, G. / Bunkoczi, G. / Uppenberg, J. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Dual specificity protein phosphatase 13 (DUSP13).
Authors: Ugochukwu, E. / Salah, E. / Savitsky, P. / Barr, A. / Pantic, N. / Niesen, F. / Burgess-Brown, N. / Berridge, G. / Bunkoczi, G. / Uppenberg, J. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C. ...Authors: Ugochukwu, E. / Salah, E. / Savitsky, P. / Barr, A. / Pantic, N. / Niesen, F. / Burgess-Brown, N. / Berridge, G. / Bunkoczi, G. / Uppenberg, J. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 5, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 13
B: Dual specificity protein phosphatase 13
C: Dual specificity protein phosphatase 13
D: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)92,5384
Polymers92,5384
Non-polymers00
Water1,65792
1
A: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)23,1351
Polymers23,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)23,1351
Polymers23,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)23,1351
Polymers23,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)23,1351
Polymers23,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.821, 73.821, 303.803
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 protein phosphatase 13 / Testis- and skeletal-muscle-specific DSP / Dual specificity phosphatase SKRP4


Mass: 23134.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP13, TMDP / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta-Phage resistant
References: UniProt: Q9UII6, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 25% PEG3350, 0.15 M Ammonium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 43981 / Num. obs: 43981 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2 / Num. unique all: 23036 / Rsym value: 0.598 / % possible all: 99.1

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GWO

2gwo


Resolution: 2.3→20 Å / Num. parameters: 21036 / Num. restraintsaints: 37224 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 2017 -RANDOM
Rwork0.1765 ---
all0.1765 41773 --
obs0.1765 41773 95.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 5088 / Occupancy sum non hydrogen: 5258
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 0 92 5258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0.058
X-RAY DIFFRACTIONs_from_restr_planes0.0241
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0

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