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- PDB-6d65: Crystal structure of the human dual specificity phosphatase 1 cat... -

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Basic information

Entry
Database: PDB / ID: 6d65
TitleCrystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein off7
Components
  • Designed AR protein off7
  • Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
KeywordsHYDROLASE / Dual specificity phosphatase / DUSP / C258S / MBP / DARPin
Function / homology
Function and homology information


negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade ...negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade / RAF-independent MAPK1/3 activation / cellular response to chemokine / negative regulation of cell adhesion / mitogen-activated protein kinase binding / growth factor binding / protein-serine/threonine phosphatase / detection of maltose stimulus / response to testosterone / maltose transport complex / negative regulation of MAP kinase activity / protein serine/threonine phosphatase activity / carbohydrate transport / peptidyl-tyrosine dephosphorylation / response to light stimulus / phosphoprotein phosphatase activity / carbohydrate transmembrane transporter activity / response to cAMP / maltose binding / maltose transport / maltodextrin transmembrane transport / response to retinoic acid / cellular response to hormone stimulus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / ATP-binding cassette (ABC) transporter complex / protein tyrosine phosphatase activity / response to glucocorticoid / cell chemotaxis / response to hydrogen peroxide / response to calcium ion / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / response to estradiol / outer membrane-bounded periplasmic space / periplasmic space / intracellular signal transduction / positive regulation of apoptotic process / negative regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / 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. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ETHANOL / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsGumpena, R. / Lountos, G.T. / Waugh, D.S.
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 off7
C: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
D: Designed AR protein off7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,55454
Polymers150,8244
Non-polymers3,72950
Water10,917606
1
A: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
B: Designed AR protein off7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,25226
Polymers75,4122
Non-polymers1,84024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
D: Designed AR protein off7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,30228
Polymers75,4122
Non-polymers1,89026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.327, 109.503, 218.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#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.: 2
Mutation: 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 off7


Mass: 18308.467 Da / Num. of mol.: 2
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 , 4 types, 656 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15 M NaCl 0.1 M sodium cacodylate 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 75855 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 17.1
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3726 / % possible all: 100

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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: 3H4Z, 3EZZ, 1SVX

3h4z

3ezz

1svx


Resolution: 2.348→38.675 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.12
RfactorNum. reflection% reflection
Rfree0.2409 3728 4.92 %
Rwork0.1851 --
obs0.1879 75783 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.348→38.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10181 0 214 611 11006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810634
X-RAY DIFFRACTIONf_angle_d0.89514428
X-RAY DIFFRACTIONf_dihedral_angle_d5.8878257
X-RAY DIFFRACTIONf_chiral_restr0.0521579
X-RAY DIFFRACTIONf_plane_restr0.0061857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3479-2.37760.30941210.2342250X-RAY DIFFRACTION85
2.3776-2.40890.30461260.22052660X-RAY DIFFRACTION100
2.4089-2.44190.30461450.22382625X-RAY DIFFRACTION100
2.4419-2.47670.27171450.21062643X-RAY DIFFRACTION100
2.4767-2.51370.27611490.20662690X-RAY DIFFRACTION100
2.5137-2.5530.29471310.21192632X-RAY DIFFRACTION100
2.553-2.59480.27841380.20562661X-RAY DIFFRACTION100
2.5948-2.63960.25061390.20632633X-RAY DIFFRACTION100
2.6396-2.68750.29491340.21162702X-RAY DIFFRACTION100
2.6875-2.73920.29611410.21612635X-RAY DIFFRACTION100
2.7392-2.79510.28471360.22512667X-RAY DIFFRACTION100
2.7951-2.85590.27011420.22752634X-RAY DIFFRACTION100
2.8559-2.92230.26481440.22762667X-RAY DIFFRACTION100
2.9223-2.99530.27981130.2362717X-RAY DIFFRACTION100
2.9953-3.07630.29791550.23282629X-RAY DIFFRACTION100
3.0763-3.16680.27781450.23562697X-RAY DIFFRACTION100
3.1668-3.26890.31441310.21412692X-RAY DIFFRACTION100
3.2689-3.38570.27091370.20242649X-RAY DIFFRACTION100
3.3857-3.52120.22821470.18572696X-RAY DIFFRACTION100
3.5212-3.68130.22561340.16752691X-RAY DIFFRACTION100
3.6813-3.87520.22531310.15222709X-RAY DIFFRACTION100
3.8752-4.11780.18851320.14482698X-RAY DIFFRACTION100
4.1178-4.43530.17741350.13532733X-RAY DIFFRACTION100
4.4353-4.88090.17271240.13322701X-RAY DIFFRACTION100
4.8809-5.58530.20961470.1532735X-RAY DIFFRACTION100
5.5853-7.030.25071420.19152771X-RAY DIFFRACTION99
7.03-38.68070.20551640.17462838X-RAY DIFFRACTION98

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