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- PDB-6d66: Crystal structure of the human dual specificity 1 catalytic domai... -

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Basic information

Entry
Database: PDB / ID: 6d66
TitleCrystal structure of the human dual specificity 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein mbp3_16
Components
  • Designed AR protein mbp3_16
  • Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
KeywordsHYDROLASE / DUSP / C258S / MBP / DARPin
Function / homology
Function and homology information


negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of p38MAPK cascade / peptidyl-serine dephosphorylation / RAF-independent MAPK1/3 activation ...negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of p38MAPK cascade / peptidyl-serine dephosphorylation / RAF-independent MAPK1/3 activation / negative regulation of cell adhesion / cellular response to chemokine / mitogen-activated protein kinase binding / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / detection of maltose stimulus / maltose transport complex / carbohydrate transport / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / carbohydrate transmembrane transporter activity / maltose binding / negative regulation of MAP kinase activity / maltose transport / maltodextrin transmembrane transport / negative regulation of MAPK cascade / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Negative regulation of MAPK pathway / outer membrane-bounded periplasmic space / periplasmic space / negative regulation of cell population proliferation / DNA damage response / signal transduction / nucleus / membrane / 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 / Ankyrin repeat-containing domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Bacterial extracellular solute-binding protein / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
D-ALANINE / GLYCINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Maltose/maltodextrin-binding periplasmic protein / Dual specificity protein phosphatase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.226 Å
AuthorsGumpena, R. / Waugh, D.S. / Lountos, G.T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: MBP-binding DARPins facilitate the crystallization of an MBP fusion protein.
Authors: Gumpena, R. / Lountos, G.T. / Waugh, D.S.
History
DepositionApr 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
B: Designed AR protein mbp3_16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,00826
Polymers71,8912
Non-polymers2,11724
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint30 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.967, 79.967, 265.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1 / MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen- ...MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen-activated protein kinase phosphatase 1 / MKP-1 / Protein-tyrosine phosphatase CL100


Mass: 57103.613 Da / Num. of mol.: 1
Mutation: D82A, K83A, E172A, N173A, K239A, E362A, D363A, C258S,D82A, K83A, E172A, N173A, K239A, E362A, D363A, C258S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P28562, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Protein Designed AR protein mbp3_16


Mass: 14787.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 8 types, 331 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M DL-glutamic acid 0.2 M DL-alanine 0.2 M -glycine 0.2 M-DL-lysine 0.2 M DL-serine 0.1 M Tris: Bicine 25% MPD 25% PEG1000 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 43247 / % possible obs: 98.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 46.4
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3697 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D65

6d65


Resolution: 2.226→36.444 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.2018 2135 4.95 %
Rwork0.1594 --
obs0.1615 43109 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.226→36.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 138 307 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075225
X-RAY DIFFRACTIONf_angle_d0.7777055
X-RAY DIFFRACTIONf_dihedral_angle_d5.5344170
X-RAY DIFFRACTIONf_chiral_restr0.047763
X-RAY DIFFRACTIONf_plane_restr0.005913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2259-2.27760.39081380.322439X-RAY DIFFRACTION91
2.2776-2.33460.20961450.17942659X-RAY DIFFRACTION100
2.3346-2.39770.23441500.17192679X-RAY DIFFRACTION100
2.3977-2.46820.20231380.16682707X-RAY DIFFRACTION100
2.4682-2.54790.23421150.16732742X-RAY DIFFRACTION100
2.5479-2.63890.22751680.17972677X-RAY DIFFRACTION100
2.6389-2.74450.21371340.17262730X-RAY DIFFRACTION100
2.7445-2.86940.20891390.1662714X-RAY DIFFRACTION100
2.8694-3.02060.22091350.17262722X-RAY DIFFRACTION100
3.0206-3.20980.2311480.16172739X-RAY DIFFRACTION100
3.2098-3.45740.21041400.16022742X-RAY DIFFRACTION100
3.4574-3.8050.1791520.14372786X-RAY DIFFRACTION100
3.805-4.35480.15461340.12592789X-RAY DIFFRACTION100
4.3548-5.48360.18121640.13842811X-RAY DIFFRACTION100
5.4836-36.44910.18891350.16623038X-RAY DIFFRACTION100

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