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- PDB-8t2j: Structure of the catalytic domain of PPM1D/Wip1 serine/threonine ... -

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Basic information

Entry
Database: PDB / ID: 8t2j
TitleStructure of the catalytic domain of PPM1D/Wip1 serine/threonine phosphatase
ComponentsProtein phosphatase 1D
KeywordsHYDROLASE / Protein phosphatase / Metal-binding protein / Cell cycle / Cancer
Function / homology
Function and homology information


regulation of transcription initiation by RNA polymerase II / peptidyl-threonine dephosphorylation / Transcriptional regulation by RUNX2 / DNA methylation-dependent heterochromatin formation / mitogen-activated protein kinase binding / myosin phosphatase activity / negative regulation of gene expression, epigenetic / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / DNA damage response, signal transduction by p53 class mediator ...regulation of transcription initiation by RNA polymerase II / peptidyl-threonine dephosphorylation / Transcriptional regulation by RUNX2 / DNA methylation-dependent heterochromatin formation / mitogen-activated protein kinase binding / myosin phosphatase activity / negative regulation of gene expression, epigenetic / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / DNA damage response, signal transduction by p53 class mediator / cellular response to starvation / protein dephosphorylation / response to bacterium / response to radiation / G2/M transition of mitotic cell cycle / negative regulation of cell population proliferation / protein serine/threonine kinase activity / nucleolus / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein phosphatase 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, J.P. / Kosek, D. / Dyda, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)Research resulting in this structure was funded in part by the Intramural Program of the NIDDK United States
CitationJournal: To Be Published
Title: Structure of the catalytic domain of PPM1D/Wip1 serine/threonine phosphatase
Authors: Kumar, J.P. / Kosek, D. / Dyda, F.
History
DepositionJun 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6006
Polymers38,2611
Non-polymers3395
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.664, 59.930, 49.566
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Protein phosphatase 1D / Protein phosphatase 2C isoform delta / PP2C-delta / Protein phosphatase magnesium-dependent 1 delta ...Protein phosphatase 2C isoform delta / PP2C-delta / Protein phosphatase magnesium-dependent 1 delta / p53-induced protein phosphatase 1


Mass: 38261.461 Da / Num. of mol.: 1 / Mutation: G8R, P33E, R250A, R258A, R259A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1D, WIP1 / Plasmid: pE-SUMOstar Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: O15297, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 10% (w/v) PEG 3000, 20% PEG 400 (v/v), and 10% glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 26792 / % possible obs: 98.9 % / Redundancy: 4.67 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Net I/σ(I): 15.75
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.850.49120100.9110.5321
1.85-1.90.37419110.9420.4041
1.9-1.950.31318550.9590.3371
1.95-2.010.23218170.9730.251
2.01-2.080.19117740.9790.2061
2.08-2.150.16317040.9810.1761
2.15-2.230.13116080.9860.1421
2.23-2.320.11215660.9930.121
2.32-2.430.09515390.9940.1021
2.43-2.550.08614730.9940.0931
2.55-2.680.07813970.9950.0841
2.68-2.850.07312980.9950.081
2.85-3.040.0712310.9950.0761
3.04-3.290.06511210.9950.0711
3.29-3.60.06210710.9950.0671
3.6-4.030.0579690.9960.0621
4.03-4.650.0558550.9970.061
4.65-5.690.0497200.9970.0541
5.69-8.050.0535570.9960.0581

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25.65 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.4976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1072 4 %
Rwork0.1747 25718 -
obs0.1764 26790 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 21 125 2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01462707
X-RAY DIFFRACTIONf_angle_d1.31593653
X-RAY DIFFRACTIONf_chiral_restr0.0891398
X-RAY DIFFRACTIONf_plane_restr0.0124471
X-RAY DIFFRACTIONf_dihedral_angle_d10.688372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.29641340.21853194X-RAY DIFFRACTION98.52
1.88-1.980.28361340.20083232X-RAY DIFFRACTION99.23
1.98-2.10.22861320.1833172X-RAY DIFFRACTION98.95
2.11-2.270.24351310.17583163X-RAY DIFFRACTION97.98
2.27-2.50.24451370.17723261X-RAY DIFFRACTION99.91
2.5-2.860.23251330.18653194X-RAY DIFFRACTION99.19
2.86-3.60.23761340.17963211X-RAY DIFFRACTION98.35
3.6-25.650.17971370.15993291X-RAY DIFFRACTION99.02

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