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- PDB-2oud: Crystal structure of the catalytic domain of human MKP5 -

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Basic information

Entry
Database: PDB / ID: 2oud
TitleCrystal structure of the catalytic domain of human MKP5
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / A central five-stranded b-sheet
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / negative regulation of JUN kinase activity / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / negative regulation of JNK cascade / positive regulation of regulatory T cell differentiation / negative regulation of stress-activated MAPK cascade / mitogen-activated protein kinase p38 binding / dephosphorylation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsTao, X. / Tong, L.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5.
Authors: Tao, X. / Tong, L.
History
DepositionFeb 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2682
Polymers20,2321
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.514, 92.514, 78.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 20232.203 Da / Num. of mol.: 1
Fragment: Tyrosine-protein phosphatase domain (Residues 315-482)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6W6, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.77 Å3/Da / Density % sol: 74.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM Bis-tris (pH 6.0), and 2.7-3.0 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 9841 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 68.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.297
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.197 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 414594.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.248 906 10.4 %RANDOM
Rwork0.213 ---
obs0.213 8690 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1219 Å2 / ksol: 0.326933 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.37 Å215.82 Å20 Å2
2--8.59 Å20 Å2
3----18.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 1 47 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 64 10.3 %
Rwork0.298 559 -
obs--64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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