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- PDB-7l4i: Crystal structure of a substrate-trapping variant of PPM1H phosphatase -

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Basic information

Entry
Database: PDB / ID: 7l4i
TitleCrystal structure of a substrate-trapping variant of PPM1H phosphatase
ComponentsProtein phosphatase 1H
KeywordsHYDROLASE / Rab GTPase / LRRK2 kinase / PP2C/PPM family / membrane trafficking
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / glutamatergic synapse / signal transduction / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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
Protein phosphatase 1H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsKhan, A.R. / Waschbusch, D.
CitationJournal: Embo Rep. / Year: 2021
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
DepositionDec 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1H
B: Protein phosphatase 1H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7336
Polymers100,6362
Non-polymers974
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-56 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.688, 101.105, 148.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein phosphatase 1H


Mass: 50317.965 Da / Num. of mol.: 2 / Mutation: D288A, C56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1H, ARHCL1, KIAA1157, URCC2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ULR3, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979279 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2019
RadiationMonochromator: 0.979279 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979279 Å / Relative weight: 1
ReflectionResolution: 2.58→28.97 Å / Num. obs: 34086 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.6 / Num. measured all: 224906
Reflection shellResolution: 2.58→2.7 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.651 / Num. unique obs: 3998 / CC1/2: 0.879 / Rpim(I) all: 0.272 / Rrim(I) all: 0.707 / % possible all: 96.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b67

6b67


Resolution: 2.58→28.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1708 5.02 %
Rwork0.1897 32310 -
obs0.1921 34018 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.78 Å2 / Biso mean: 57.6578 Å2 / Biso min: 27.45 Å2
Refinement stepCycle: final / Resolution: 2.58→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6257 0 4 91 6352
Biso mean--56.31 56.62 -
Num. residues----790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.58-2.660.28971390.2445254695
2.66-2.750.28531390.23612655100
2.75-2.840.29591440.23762652100
2.84-2.960.31241350.22582677100
2.96-3.090.27931370.2272680100
3.09-3.250.29021350.21992691100
3.25-3.460.27821490.20632666100
3.46-3.730.26781460.18642706100
3.73-4.10.23731320.17552708100
4.1-4.690.20711450.15462725100
4.69-5.90.1941420.17432758100
Refinement TLS params.Method: refined / Origin x: 16.9335 Å / Origin y: 60.984 Å / Origin z: 95.9169 Å
111213212223313233
T0.3309 Å20.0267 Å2-0.0164 Å2-0.311 Å2-0.0009 Å2--0.3656 Å2
L0.3937 °2-0.0289 °2-0.1232 °2-0.3694 °2-0.271 °2--1.351 °2
S0.0235 Å °0.043 Å °0.0105 Å °0.0327 Å °-0.0656 Å °-0.0106 Å °-0.0371 Å °0.1015 Å °0.0403 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 601
2X-RAY DIFFRACTION1allB35 - 601
3X-RAY DIFFRACTION1allS2 - 107

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