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- PDB-9hab: Crystal structure of a chimeric PPM1H phosphatase with the flap d... -

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Basic information

Entry
Database: PDB / ID: 9hab
TitleCrystal structure of a chimeric PPM1H phosphatase with the flap domain of PPM1J
ComponentsPPM1H metal-dependent Ser/Thr phosphatase
KeywordsHYDROLASE / phosphatase / phospho-Rab hydrolase / enzyme / membrane trafficking / Parkinson's disease LRRK2 kinase
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsKhan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland20/FFP-A/8446 Ireland
Citation
Journal: To Be Published
Title: Crystal structure of a chimeric PPM1H phosphatase with the flap domain of PPM1J
Authors: Khan, A.R.
#1: Journal: Br. J. Pharmacol.
Title: Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.
Authors: Waschbusch, D. / Berndsen, K. / Lis, P. / Knebel, A. / Lam, Y.P. / Alessi, D.R. / Khan, A.R.
History
DepositionNov 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PPM1H metal-dependent Ser/Thr phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3474
Polymers50,1821
Non-polymers1653
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, static light scattering coupled to gel filtration chromatorgraphy confirmed dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-16 kcal/mol
Surface area17610 Å2
Unit cell
Length a, b, c (Å)110.093, 110.093, 87.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PPM1H metal-dependent Ser/Thr phosphatase


Mass: 50182.121 Da / Num. of mol.: 1 / Mutation: chimera of FLAP domain of PPM1J
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: 30% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.86→110.09 Å / Num. obs: 12945 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 16.9
Reflection shellResolution: 2.86→3.01 Å / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 2.215 / Num. measured all: 24178 / Num. unique obs: 1848 / CC1/2: 0.496 / Rpim(I) all: 0.632 / Rrim(I) all: 2.305 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→77.85 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 36.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 1163 4.89 %
Rwork0.2422 --
obs0.2439 12945 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 3 3 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d17.6451160
X-RAY DIFFRACTIONf_chiral_restr0.048470
X-RAY DIFFRACTIONf_plane_restr0.027541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.990.4381520.42452846X-RAY DIFFRACTION100
2.99-3.150.40311240.36332848X-RAY DIFFRACTION100
3.15-3.350.37711630.30672793X-RAY DIFFRACTION100
3.35-3.60.33371610.31062819X-RAY DIFFRACTION100
3.6-3.970.31651180.26312838X-RAY DIFFRACTION100
3.97-4.540.30141500.22912816X-RAY DIFFRACTION100
4.54-5.720.22051300.22122850X-RAY DIFFRACTION100
5.72-77.850.23121650.20032798X-RAY DIFFRACTION100

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