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- PDB-2gwo: crystal structure of TMDP -

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Basic information

Entry
Database: PDB / ID: 2gwo
Titlecrystal structure of TMDP
ComponentsDual specificity protein phosphatase 13
KeywordsHYDROLASE / alpha/beta
Function / homology
Function and homology information


MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of MAPK cascade / myosin phosphatase activity / 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 / negative regulation of MAPK cascade / myosin phosphatase activity / 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: 2.4 Å
AuthorsKim, S.J. / Ryu, S.E. / Kim, J.H.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of human TMDP, a testis-specific dual specificity protein phosphatase: implications for substrate specificity
Authors: Kim, S.J. / Jeong, D.G. / Yoon, T.S. / Son, J.H. / Cho, S.K. / Ryu, S.E. / Kim, J.H.
History
DepositionMay 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)88,6984
Polymers88,6984
Non-polymers00
Water4,684260
1
A: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 13


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.586, 72.240, 89.896
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dual specificity protein phosphatase 13 / Testis- and skeletal-muscle-specific DSP / Dual specificity phosphatase SKRP4 / TMDP


Mass: 22174.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP13, TMDP / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UII6, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M NaCl, 10% EtOH, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2002
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 30615 / Num. obs: 29452 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.4 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 1443 RANDOM
Rwork0.198 --
obs0.198 29446 -
all-29452 -
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 0 260 5642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_dihedral_angle_d22

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