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- PDB-9d14: Tt Pah2 D148N delta helix with magnesium -

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Basic information

Entry
Database: PDB / ID: 9d14
TitleTt Pah2 D148N delta helix with magnesium
ComponentsNuclear elongation and deformation protein
KeywordsHYDROLASE / lipin Pah phosphatidic acid phosphatase / lipid phosphatase
Function / homology
Function and homology information


phosphatidate phosphatase activity / metal ion binding
Similarity search - Function
Lipin, N-terminal / Lipin/Ned1/Smp2 (LNS2) / LIPIN family / lipin, N-terminal conserved region / LNS2 (Lipin/Ned1/Smp2) / LNS2/PITP / LNS2 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Nuclear elongation and deformation protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsVitkovska, T. / Khayyo, V.I. / Airola, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structures of a lipin/Pah phosphatidic acid phosphatase in distinct catalytic states reveal a signature motif for substrate recognition.
Authors: Vitkovska, T. / Welcome, F.S. / Khayyo, V.I. / Gao, S. / Wymore, T. / Airola, M.V.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
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: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5963
Polymers34,4801
Non-polymers1162
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.812, 60.812, 159.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein Nuclear elongation and deformation protein / Phosphatidic acid phosphohydrolase / Pah2


Mass: 34479.613 Da / Num. of mol.: 1 / Mutation: D148N
Source method: isolated from a genetically manipulated source
Details: Tt Pah2 residues 21-321, D148N / Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TTHERM_00215970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: I7MFJ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3000, 0.1 M CHES pH 8.5 - 9.5 + soak with 50 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.88→56.83 Å / Num. obs: 25300 / % possible obs: 97.23 % / Redundancy: 12.2 % / Biso Wilson estimate: 34.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06531 / Rpim(I) all: 0.01959 / Rrim(I) all: 0.06826 / Net I/σ(I): 18.65
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.345 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2285 / CC1/2: 0.761 / CC star: 0.93 / Rpim(I) all: 0.3935 / Rrim(I) all: 1.402 / % possible all: 92.29

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→56.83 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 20.5354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 1237 5.03 %
Rwork0.1724 23364 -
obs0.1739 24601 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.42 Å2
Refinement stepCycle: LAST / Resolution: 1.88→56.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 7 165 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01432337
X-RAY DIFFRACTIONf_angle_d1.08673154
X-RAY DIFFRACTIONf_chiral_restr0.078355
X-RAY DIFFRACTIONf_plane_restr0.0104401
X-RAY DIFFRACTIONf_dihedral_angle_d5.6255309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.960.28721240.22872429X-RAY DIFFRACTION92.53
1.96-2.040.24291370.21262446X-RAY DIFFRACTION94.72
2.04-2.150.25691370.19472512X-RAY DIFFRACTION95.91
2.15-2.290.23421470.17922522X-RAY DIFFRACTION96.95
2.29-2.460.19911310.17232567X-RAY DIFFRACTION96.98
2.46-2.710.23171180.17882628X-RAY DIFFRACTION98.49
2.71-3.10.20431330.17682665X-RAY DIFFRACTION99.36
3.1-3.910.18731470.16152717X-RAY DIFFRACTION99.86
3.91-56.830.18931630.16422878X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: -8.34837237178 Å / Origin y: -22.2767818973 Å / Origin z: -18.6122132516 Å
111213212223313233
T0.221723946284 Å2-0.0343907045823 Å2-0.020887952982 Å2-0.177326144239 Å2-0.0579973424659 Å2--0.235065013177 Å2
L2.12223671461 °20.967674455569 °2-0.0433568054084 °2-2.57910690957 °2-0.519896954598 °2--3.12448430783 °2
S0.0051522757663 Å °-0.079849518093 Å °0.0303746838639 Å °0.0134825938203 Å °-0.110617304196 Å °0.030362346741 Å °0.0242976355906 Å °-0.0561017782172 Å °0.0635040227794 Å °
Refinement TLS groupSelection details: all

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