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- PDB-7kiq: Crystal structure of the mouse lipin-2 M-Lip domain -

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Basic information

Entry
Database: PDB / ID: 7kiq
TitleCrystal structure of the mouse lipin-2 M-Lip domain
ComponentsPhosphatidate phosphatase LPIN2
KeywordsLIPID BINDING PROTEIN / lipin / M-Lip / dimer
Function / homology
Function and homology information


Synthesis of PE / Triglyceride biosynthesis / phosphatidate phosphatase / phosphatidate phosphatase activity / Synthesis of PC / Depolymerization of the Nuclear Lamina / triglyceride biosynthetic process / cellular lipid metabolic process / fatty acid catabolic process / lipid metabolic process ...Synthesis of PE / Triglyceride biosynthesis / phosphatidate phosphatase / phosphatidate phosphatase activity / Synthesis of PC / Depolymerization of the Nuclear Lamina / triglyceride biosynthetic process / cellular lipid metabolic process / fatty acid catabolic process / lipid metabolic process / cellular response to insulin stimulus / transcription coactivator activity / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Lipin, middle domain / Lipin/Ned1/Smp2 multi-domain protein middle domain / Lipin, N-terminal / Lipin/Ned1/Smp2 (LNS2) / LIPIN family / LNS2/PITP / lipin, N-terminal conserved region / LNS2 (Lipin/Ned1/Smp2) / LNS2 / HAD-like superfamily
Similarity search - Domain/homology
Phosphatidate phosphatase LPIN2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.523 Å
AuthorsYang, J.W. / Gu, W. / Airola, M.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
American Heart Association17SDG33410860 United States
CitationJournal: Nat Commun / Year: 2021
Title: The middle lipin domain adopts a membrane-binding dimeric protein fold.
Authors: Gu, W. / Gao, S. / Wang, H. / Fleming, K.D. / Hoffmann, R.M. / Yang, J.W. / Patel, N.M. / Choi, Y.M. / Burke, J.E. / Reue, K. / Airola, M.V.
History
DepositionOct 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: 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

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Assembly

Deposited unit
A: Phosphatidate phosphatase LPIN2
B: Phosphatidate phosphatase LPIN2
C: Phosphatidate phosphatase LPIN2
D: Phosphatidate phosphatase LPIN2
E: Phosphatidate phosphatase LPIN2
F: Phosphatidate phosphatase LPIN2
G: Phosphatidate phosphatase LPIN2
H: Phosphatidate phosphatase LPIN2
I: Phosphatidate phosphatase LPIN2
J: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,93020
Polymers103,52910
Non-polymers40110
Water4,576254
1
A: Phosphatidate phosphatase LPIN2
B: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7864
Polymers20,7062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-46 kcal/mol
Surface area9290 Å2
MethodPISA
2
C: Phosphatidate phosphatase LPIN2
D: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7864
Polymers20,7062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-42 kcal/mol
Surface area9540 Å2
MethodPISA
3
E: Phosphatidate phosphatase LPIN2
F: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7864
Polymers20,7062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-44 kcal/mol
Surface area9280 Å2
MethodPISA
4
G: Phosphatidate phosphatase LPIN2
H: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7864
Polymers20,7062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-46 kcal/mol
Surface area9130 Å2
MethodPISA
5
I: Phosphatidate phosphatase LPIN2
hetero molecules

J: Phosphatidate phosphatase LPIN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7864
Polymers20,7062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area2720 Å2
ΔGint-47 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.706, 84.612, 97.511
Angle α, β, γ (deg.)90.000, 108.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphatidate phosphatase LPIN2 / Lipin-2


Mass: 10352.913 Da / Num. of mol.: 10 / Fragment: M-Lip domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lpin2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q99PI5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.67 Å3/Da / Density % sol: 53.85 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 3350, CaAcetate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.523→51.65 Å / Num. obs: 36291 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.105 / Rrim(I) all: 0.277 / Net I/σ(I): 5.5
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.124 / Num. measured all: 18637 / Num. unique obs: 2634 / CC1/2: 0.62 / Rpim(I) all: 0.856 / Rrim(I) all: 2.291 / Net I/σ(I) obs: 1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KIH

7kih


Resolution: 2.523→47.353 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1842 5.09 %
Rwork0.2122 34369 -
obs0.2142 36211 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.97 Å2 / Biso mean: 52.7316 Å2 / Biso min: 24.55 Å2
Refinement stepCycle: final / Resolution: 2.523→47.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 43 254 6847
Biso mean--83.76 49.8 -
Num. residues----806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.523-2.5910.32881180.3257239991
2.591-2.66730.37771370.2997262299
2.6673-2.75340.36411600.3019265199
2.7534-2.85170.32861620.2883261699
2.8517-2.96590.37971320.2583265499
2.9659-3.10090.29071400.2439262899
3.1009-3.26430.27041210.2272269499
3.2643-3.46880.23931140.2064266799
3.4688-3.73650.24261560.1884267699
3.7365-4.11230.21071530.1876265299
4.1123-4.70690.21171400.15992696100
4.7069-5.92840.21641480.18882699100
5.9284-47.3530.21871610.2039271599

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