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- PDB-9d15: Tt Pah2 D148N delta helix with magnesium and tungstate -

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Basic information

Entry
Database: PDB / ID: 9d15
TitleTt Pah2 D148N delta helix with magnesium and tungstate
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
TUNGSTATE(VI)ION / Nuclear elongation and deformation protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0925
Polymers34,4801
Non-polymers6124
Water1,71195
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)60.293, 60.293, 158.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
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 and 5 mM sodium tungstate

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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: 2.25→60.29 Å / Num. obs: 26448 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 41.38 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.2127 / Rpim(I) all: 0.0637 / Rrim(I) all: 0.2223 / Net I/σ(I): 11.74
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 12.5 % / Rmerge(I) obs: 3.211 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1412 / CC1/2: 0.643 / CC star: 0.885 / Rpim(I) all: 0.9443 / Rrim(I) all: 3.349 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→60.29 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1315 4.97 %
Rwork0.1995 --
obs0.2016 26448 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→60.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 10 95 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032327
X-RAY DIFFRACTIONf_angle_d0.5513143
X-RAY DIFFRACTIONf_dihedral_angle_d18.98889
X-RAY DIFFRACTIONf_chiral_restr0.049354
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.36451250.28722795X-RAY DIFFRACTION100
2.34-2.450.27651440.25192803X-RAY DIFFRACTION100
2.45-2.580.26631450.24272771X-RAY DIFFRACTION100
2.58-2.740.33121510.24122821X-RAY DIFFRACTION100
2.74-2.950.26681800.22942733X-RAY DIFFRACTION100
2.95-3.250.26621230.20462826X-RAY DIFFRACTION100
3.25-3.710.23061310.18152809X-RAY DIFFRACTION100
3.72-4.680.23551690.15712773X-RAY DIFFRACTION100
4.68-60.290.18851470.19472802X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.4253 Å / Origin y: 7.9625 Å / Origin z: -18.3937 Å
111213212223313233
T0.1993 Å2-0.0279 Å2-0.03 Å2-0.1817 Å2-0.0417 Å2--0.2343 Å2
L2.4498 °21.1462 °2-0.4205 °2-2.5327 °2-0.6785 °2--3.3953 °2
S0.0005 Å °-0.0366 Å °0.0802 Å °0.0689 Å °-0.0974 Å °-0.0199 Å °-0.1516 Å °-0.0294 Å °0.0338 Å °
Refinement TLS groupSelection details: all

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