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- PDB-7l4j: Crystal structure of WT PPM1H phosphatase -

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Basic information

Entry
Database: PDB / ID: 7l4j
TitleCrystal structure of WT PPM1H phosphatase
ComponentsProtein phosphatase 1H
KeywordsHYDROLASE / Rab GTPase / LRRK2 kinase / 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: 2.451 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)100,8216
Polymers100,7242
Non-polymers974
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-54 kcal/mol
Surface area32990 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: 50361.977 Da / Num. of mol.: 2 / Mutation: 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.: 115 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: 0.1M imidazole 20% jeffamine ED-2001 / PH range: 7

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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: 0.979354 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979354 Å / Relative weight: 1
ReflectionResolution: 2.45→28.97 Å / Num. obs: 74295 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 14.6
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.781 / Num. unique obs: 3324 / CC1/2: 0.779 / Rpim(I) all: 0.321 / Rrim(I) all: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b67

6b67


Resolution: 2.451→28.966 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 3736 5.03 %
Rwork0.1902 70559 -
obs0.1927 39355 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.47 Å2 / Biso mean: 60.4708 Å2 / Biso min: 29.07 Å2
Refinement stepCycle: final / Resolution: 2.451→28.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 4 115 6374
Biso mean--45.14 56.7 -
Num. residues----789
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4513-2.48230.346770.303145955
2.4823-2.51490.35991430.27542711100
2.5149-2.54930.29841400.26522604100
2.5493-2.58570.35571400.27092645100
2.5857-2.62430.27371300.25832714100
2.6243-2.66530.33691660.2542615100
2.6653-2.7090.31191430.25312656100
2.709-2.75560.30991270.25572671100
2.7556-2.80570.31051430.25322704100
2.8057-2.85960.32781320.24262630100
2.8596-2.91790.29981440.2222644100
2.9179-2.98130.33331280.23482665100
2.9813-3.05060.30321550.23272685100
3.0506-3.12680.26471310.22652622100
3.1268-3.21120.28061260.21772700100
3.2112-3.30560.25471360.21782634100
3.3056-3.41210.29931630.21592659100
3.4121-3.53390.23171400.20272669100
3.5339-3.67510.35431270.2262999
3.6751-3.8420.2461360.1887266999
3.842-4.04410.26151450.17512650100
4.0441-4.29670.20821520.15792631100
4.2967-4.62720.21061230.14362685100
4.6272-5.09060.1641490.1462670100
5.0906-5.8220.20971410.16212648100
5.822-7.31550.19511440.15712657100
Refinement TLS params.Method: refined / Origin x: -17.5354 Å / Origin y: 10.7873 Å / Origin z: -21.3942 Å
111213212223313233
T0.236 Å2-0.0312 Å2-0.0354 Å2-0.2539 Å2-0.0315 Å2--0.3405 Å2
L0.6568 °2-0.0146 °2-0.3342 °2-0.7792 °20.0342 °2--2.2431 °2
S0.0153 Å °-0.0021 Å °-0.0155 Å °0.0206 Å °-0.0699 Å °0.0568 Å °-0.0017 Å °-0.1125 Å °0.0514 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 601
2X-RAY DIFFRACTION1allB34 - 601
3X-RAY DIFFRACTION1allS1 - 135

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