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- PDB-2ouc: Crystal structure of the MAP kinase binding domain of MKP5 -

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Basic information

Entry
Database: PDB / ID: 2ouc
TitleCrystal structure of the MAP kinase binding domain of MKP5
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / Rhodanese fold
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / 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 / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / JUN kinase binding / negative regulation of JNK cascade / positive regulation of regulatory T cell differentiation / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / 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 / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain ...Mitogen-activated protein (MAP) kinase phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
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
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)32,4682
Polymers32,4682
Non-polymers00
Water2,072115
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)16,2341
Polymers16,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)16,2341
Polymers16,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.296, 52.164, 62.267
Angle α, β, γ (deg.)90.00, 89.36, 90.00
Int Tables number4
Space group name H-MP1211

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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: 16233.819 Da / Num. of mol.: 2 / Fragment: Rhodanese domain (Residues 148-287)
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate (pH 4.5), and 2.3-2.5 M ammonium acetate, 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: 2.2→30 Å / Num. obs: 31415 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.1234
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.411 / % possible all: 88.4

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Processing

Software
NameVersionClassification
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 579830.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2726 9.6 %RANDOM
Rwork0.232 ---
obs0.232 28451 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5309 Å2 / ksol: 0.357953 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å21.31 Å2
2--8.63 Å20 Å2
3----11.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 0 116 2242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.312 233 10.3 %
Rwork0.268 2021 -
obs--71.2 %
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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