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- PDB-7kpr: Structure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 7kpr
TitleStructure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution
ComponentsProtein phosphatase 1H
KeywordsHYDROLASE / Rab GTPase / membrane trafficking / PPM family
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: 3.09 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
DepositionNov 12, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,8796
Polymers107,7822
Non-polymers974
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-56 kcal/mol
Surface area34120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.684, 102.160, 148.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 35 through 104 or resid 142 through 183 or resid 235 through 511))
d_2ens_1(chain "B" and resid 35 through 511)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEULYSA1 - 70
d_12ens_1VALASNA72 - 113
d_13ens_1ILEASNA127 - 403
d_21ens_1LEUASNB3 - 391

NCS oper: (Code: givenMatrix: (0.381201247254, -0.73465906491, 0.561214457617), (-0.727955782525, -0.612731068418, -0.307637800805), (0.569882433297, -0.291267396289, -0.768373161997)Vector: 7. ...NCS oper: (Code: given
Matrix: (0.381201247254, -0.73465906491, 0.561214457617), (-0.727955782525, -0.612731068418, -0.307637800805), (0.569882433297, -0.291267396289, -0.768373161997)
Vector: 7.20691578104, 37.6435359477, 30.3207356133)

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Components

#1: Protein Protein phosphatase 1H


Mass: 53890.961 Da / Num. of mol.: 2
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.: 14 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.5 / Details: 10% isopropanol, 5% PEG4000, 0.05M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.09→28.78 Å / Num. obs: 19927 / % possible obs: 99.25 % / Redundancy: 6.7 % / Biso Wilson estimate: 92.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Net I/σ(I): 19.83
Reflection shellResolution: 3.09→3.2 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 1853 / CC1/2: 0.855 / Rrim(I) all: 0.84

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b67

6b67


Resolution: 3.09→28.78 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 26.0137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1876 5.04 %random
Rwork0.1956 35317 --
obs0.1969 19925 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.63 Å2
Refinement stepCycle: LAST / Resolution: 3.09→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 4 14 6302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486416
X-RAY DIFFRACTIONf_angle_d0.96378688
X-RAY DIFFRACTIONf_chiral_restr0.0552966
X-RAY DIFFRACTIONf_plane_restr0.00561126
X-RAY DIFFRACTIONf_dihedral_angle_d17.00992386
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.765726149409 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.34881160.31662498X-RAY DIFFRACTION89.92
3.17-3.270.35351500.26552681X-RAY DIFFRACTION99.89
3.27-3.370.34191350.26082758X-RAY DIFFRACTION99.86
3.37-3.490.26761640.25362733X-RAY DIFFRACTION100
3.49-3.630.30111450.23112748X-RAY DIFFRACTION99.93
3.63-3.80.25471390.22292743X-RAY DIFFRACTION99.86
3.8-40.2511460.22242751X-RAY DIFFRACTION99.93
4-4.250.23671400.19472726X-RAY DIFFRACTION99.83
4.25-4.570.20031410.17422740X-RAY DIFFRACTION99.97
4.57-5.030.21391440.17192740X-RAY DIFFRACTION100
5.03-5.750.19571430.18592744X-RAY DIFFRACTION100
5.75-7.230.19531520.19292737X-RAY DIFFRACTION99.93
7.23-28.780.1631610.15192718X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 17.8518424065 Å / Origin y: 10.743001406 Å / Origin z: 21.1718562482 Å
111213212223313233
T0.472585317447 Å20.0619944372486 Å20.0649450871998 Å2-0.472185952572 Å20.0431679457556 Å2--0.631022846108 Å2
L1.11555441961 °2-0.142973961229 °2-0.372904666338 °2-1.57698596408 °2-0.0876153718651 °2--2.77932688667 °2
S-0.116245089978 Å °-0.0704872290804 Å °-0.267488953275 Å °0.291624798016 Å °-0.143067390238 Å °0.0777918168118 Å °0.265986611439 Å °0.19848423494 Å °0.252419867076 Å °
Refinement TLS groupSelection details: all

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