[English] 日本語
Yorodumi
- PDB-9d13: Tt Pah2 D148N delta helix apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d13
TitleTt Pah2 D148N delta helix apo
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: 1.98 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5722
Polymers34,4801
Non-polymers921
Water1,874104
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)60.779, 60.779, 159.474
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

-
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 3000, 0.1 M CHES pH 8.5 - 9.5

-
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: 1.98→60.78 Å / Num. obs: 21672 / % possible obs: 99.79 % / Redundancy: 12.2 % / Biso Wilson estimate: 40.41 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09526 / Rpim(I) all: 0.02848 / Rrim(I) all: 0.09957 / Net I/σ(I): 14.78
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.157 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 2110 / CC1/2: 0.67 / CC star: 0.896 / Rpim(I) all: 0.6363 / Rrim(I) all: 2.251 / % possible all: 99.39

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→60.78 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1957 4.93 %
Rwork0.1923 37760 -
obs0.1936 21660 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.77 Å2
Refinement stepCycle: LAST / Resolution: 1.98→60.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 6 104 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172274
X-RAY DIFFRACTIONf_angle_d1.00233069
X-RAY DIFFRACTIONf_chiral_restr0.0564343
X-RAY DIFFRACTIONf_plane_restr0.021391
X-RAY DIFFRACTIONf_dihedral_angle_d5.9068300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.28381630.29472716X-RAY DIFFRACTION99.55
2.03-2.080.30541070.25312685X-RAY DIFFRACTION99.64
2.08-2.150.2522840.2462722X-RAY DIFFRACTION99.57
2.15-2.220.2507980.24492756X-RAY DIFFRACTION99.69
2.22-2.290.2731510.24892661X-RAY DIFFRACTION99.82
2.29-2.390.26251620.20772702X-RAY DIFFRACTION99.86
2.39-2.490.24931240.20812681X-RAY DIFFRACTION100
2.49-2.630.26351710.20862692X-RAY DIFFRACTION99.9
2.63-2.790.26811640.21462667X-RAY DIFFRACTION99.89
2.79-3.010.23231360.19612710X-RAY DIFFRACTION100
3.01-3.310.25721380.18942704X-RAY DIFFRACTION100
3.31-3.790.18531150.17012734X-RAY DIFFRACTION100
3.79-4.770.18011620.14882667X-RAY DIFFRACTION100
4.77-60.780.19531820.19852663X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 21.7870815321 Å / Origin y: 7.75432270096 Å / Origin z: -18.4079615349 Å
111213212223313233
T0.241462150581 Å2-0.0278628813509 Å2-0.0200636248224 Å2-0.204433462678 Å2-0.0393629270054 Å2--0.25995195846 Å2
L1.74546303854 °20.851232163514 °20.0290014961489 °2-1.95075068057 °2-0.224980069437 °2--2.79453889106 °2
S0.0467078950592 Å °-0.0855199058083 Å °0.0243999870848 Å °0.116452352068 Å °-0.108525096197 Å °0.00549460623029 Å °-0.0395854941171 Å °-0.0708405307083 Å °0.0484656478973 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more