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- PDB-7n0z: Structure of PPM1H phosphatase with manganese ions at the active site -

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Basic information

Entry
Database: PDB / ID: 7n0z
TitleStructure of PPM1H phosphatase with manganese ions at the active site
ComponentsProtein phosphatase 1H
KeywordsHYDROLASE
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: 2.19 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
DepositionMay 26, 2021Deposition 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)101,10210
Polymers100,7242
Non-polymers3788
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-57 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.779, 101.159, 148.946
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 100mM Tris-Cl 15% reagent alcohol 10mM MnCl2

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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: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.19→63.93 Å / Num. obs: 365198 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.19-2.266.71.00741530.7550.4151.09193.6
9.31-63.9360.0378400.9980.0160.04199.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7l4j

7l4j


Resolution: 2.19→63.93 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 4703 4.55 %
Rwork0.1945 98751 -
obs0.1962 103454 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.87 Å2 / Biso mean: 57.0325 Å2 / Biso min: 31.69 Å2
Refinement stepCycle: final / Resolution: 2.19→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 8 211 6435
Biso mean--48.74 52.5 -
Num. residues----785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.220.37391060.29951991209760
2.22-2.240.27791590.280733453504100
2.24-2.270.3551570.281133563513100
2.27-2.30.31251590.284833583517100
2.3-2.330.30541600.26863385354599
2.33-2.360.33031610.280733763537100
2.36-2.40.31131560.273277343399
2.4-2.430.30791620.27433533515100
2.43-2.470.34781560.27973353350999
2.47-2.510.31941580.2643312347098
2.51-2.550.33361540.25863290344498
2.55-2.60.28151630.2443356351999
2.6-2.650.29391580.226733603518100
2.65-2.710.27821540.22443333348799
2.71-2.760.30971600.22153362352299
2.76-2.830.27831600.233351351199
2.83-2.90.26091630.219233523515100
2.9-2.980.25591560.22123347350399
2.98-3.060.30731610.24373355351699
3.06-3.160.24171660.22613353351999
3.16-3.280.29541550.21443279343499
3.28-3.410.21491620.19843337349999
3.41-3.560.23121600.1863301346198
3.56-3.750.21171550.17933325348098
3.75-3.990.21321600.17533315347599
3.99-4.290.18261570.14723317347499
4.29-4.730.16761630.14113378354199
4.73-5.410.18391530.15323296344999
5.41-6.810.23091610.18363309347098
6.81-63.930.16661480.16363329347799
Refinement TLS params.Method: refined / Origin x: -17.225 Å / Origin y: 10.8006 Å / Origin z: -21.3186 Å
111213212223313233
T0.3438 Å2-0.0185 Å2-0.0071 Å2-0.347 Å2-0.0103 Å2--0.4265 Å2
L0.386 °20.0254 °2-0.155 °2-0.4922 °20.239 °2--1.545 °2
S0.0195 Å °-0.0332 Å °0.0061 Å °-0.048 Å °-0.0608 Å °-0.028 Å °-0.035 Å °-0.0623 Å °0.0402 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 512
2X-RAY DIFFRACTION1allB34 - 513
3X-RAY DIFFRACTION1allC1 - 6
4X-RAY DIFFRACTION1allS2 - 223
5X-RAY DIFFRACTION1allD1 - 2

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