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- PDB-3lj8: Crystal Structure of MKP-4 -

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Basic information

Entry
Database: PDB / ID: 3lj8
TitleCrystal Structure of MKP-4
ComponentsTyrosine-protein phosphatase
KeywordsHYDROLASE / alpha/beta hydrolase / Protein phosphatase
Function / homology
Function and homology information


MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity ...MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / JNK cascade / ERK1 and ERK2 cascade / protein dephosphorylation / protein-tyrosine-phosphatase / Negative regulation of MAPK pathway / MAPK cascade / 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 / Dual specificity protein phosphatase domain profile. / 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 / Dual specificity protein phosphatase domain profile. / 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJeong, D.G. / Yoon, T.S. / Jung, S.-K. / Park, H.S. / Ryu, S.E. / Kim, S.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Exploring binding sites other than the catalytic core in the crystal structure of the catalytic domain of MKP-4
Authors: Jeong, D.G. / Yoon, T.S. / Jung, S.-K. / Park, B.C. / Park, H.S. / Ryu, S.E. / Kim, S.J.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
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: Tyrosine-protein phosphatase


Theoretical massNumber of molelcules
Total (without water)16,6521
Polymers16,6521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.926, 91.926, 56.605
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 Tyrosine-protein phosphatase / MKP-4 / Mitogen-activated protein kinase phosphatase 4 / MAP kinase phosphatase 4


Mass: 16652.029 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 202-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q99956, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase

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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: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% ethanol, 1.3M NaCl, 0.2M MgSO4, 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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2005 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 7864 / Num. obs: 7730 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1zzw

1zzw


Resolution: 2.7→35.68 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 420 -random
Rwork0.238 ---
all0.245 7864 --
obs0.241 7646 97.7 %-
Displacement parametersBiso mean: 67.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 0 1175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9

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