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- PDB-9d16: Tt Pah2 D155N calcium -

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Basic information

Entry
Database: PDB / ID: 9d16
TitleTt Pah2 D155N calcium
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: 2.4 Å
AuthorsVitkovska, T. / 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
B: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7316
Polymers73,4662
Non-polymers2644
Water2,072115
1
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8653
Polymers36,7331
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8653
Polymers36,7331
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.277, 90.042, 109.503
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

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Components

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


Mass: 36733.176 Da / Num. of mol.: 2 / Mutation: D155N
Source method: isolated from a genetically manipulated source
Details: Tt Pah2 residues 1-321, D155N / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.1 MES pH 6, and 0.2 M calcium acetate

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 23, 2023 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.4→69.55 Å / Num. obs: 30560 / % possible obs: 99.87 % / Redundancy: 13.5 % / Biso Wilson estimate: 53.44 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1912 / Rpim(I) all: 0.05417 / Rrim(I) all: 0.1989 / Net I/σ(I): 8.97
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.9 % / Rmerge(I) obs: 2.43 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 3035 / CC1/2: 0.565 / CC star: 0.85 / Rpim(I) all: 0.6994 / Rrim(I) all: 2.531 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→69.55 Å / SU ML: 0.2938 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 2841 4.92 %
Rwork0.2142 54845 -
obs0.2157 30560 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→69.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 0 14 115 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474786
X-RAY DIFFRACTIONf_angle_d0.62896446
X-RAY DIFFRACTIONf_chiral_restr0.0464713
X-RAY DIFFRACTIONf_plane_restr0.0071818
X-RAY DIFFRACTIONf_dihedral_angle_d5.0114628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.33771490.34442782X-RAY DIFFRACTION99.9
2.44-2.490.33471440.32042753X-RAY DIFFRACTION99.86
2.49-2.530.32941350.3062715X-RAY DIFFRACTION100
2.53-2.590.31241340.31172737X-RAY DIFFRACTION100
2.59-2.640.30981510.30782768X-RAY DIFFRACTION99.97
2.64-2.70.39651510.29292701X-RAY DIFFRACTION100
2.7-2.770.32431520.27782759X-RAY DIFFRACTION99.86
2.77-2.850.35811200.25812749X-RAY DIFFRACTION99.97
2.85-2.930.25031680.23562708X-RAY DIFFRACTION99.97
2.93-3.020.23461160.23062754X-RAY DIFFRACTION99.86
3.02-3.130.27291740.23442709X-RAY DIFFRACTION99.93
3.13-3.260.25861170.22782754X-RAY DIFFRACTION100
3.26-3.410.30461620.2232750X-RAY DIFFRACTION99.93
3.41-3.590.25471580.20582739X-RAY DIFFRACTION99.97
3.59-3.810.19061310.18732744X-RAY DIFFRACTION99.9
3.81-4.10.23951340.18142743X-RAY DIFFRACTION99.86
4.1-4.520.17441420.16252750X-RAY DIFFRACTION99.9
4.52-5.170.1791260.16592757X-RAY DIFFRACTION100
5.17-6.510.24021600.20452720X-RAY DIFFRACTION99.97
6.51-69.550.21511170.22372753X-RAY DIFFRACTION99.14
Refinement TLS params.Method: refined / Origin x: -38.8351705614 Å / Origin y: -16.9624182185 Å / Origin z: 25.2376146279 Å
111213212223313233
T0.408207597599 Å2-0.0715099347928 Å20.00178363144623 Å2-0.295798518853 Å20.0105884099041 Å2--0.280947590544 Å2
L2.31775786535 °2-0.596490840755 °20.131594801273 °2-0.798736057672 °20.0308890148699 °2--0.397075966744 °2
S0.0651159293195 Å °-0.112751466008 Å °-0.0395980085983 Å °-0.0155140079286 Å °-0.0492241994434 Å °-0.00311288662552 Å °0.00931453785651 Å °0.00340738542119 Å °-0.0146133435583 Å °
Refinement TLS groupSelection details: all

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