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- PDB-5xsz: Crystal structure of zebrafish lysophosphatidic acid receptor LPA6 -

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Basic information

Entry
Database: PDB / ID: 5xsz
TitleCrystal structure of zebrafish lysophosphatidic acid receptor LPA6
ComponentsLysophosphatidic acid receptor 6a,Endolysin,Lysophosphatidic acid receptor 6a
KeywordsMEMBRANE PROTEIN / alpha helical
Function / homology
Function and homology information


P2Y receptors / G alpha (q) signalling events / lysophosphatidic acid receptor activity / positive regulation of Rho protein signal transduction / viral release from host cell by cytolysis / peptidoglycan catabolic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...P2Y receptors / G alpha (q) signalling events / lysophosphatidic acid receptor activity / positive regulation of Rho protein signal transduction / viral release from host cell by cytolysis / peptidoglycan catabolic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / host cell cytoplasm / defense response to bacterium / plasma membrane
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Lysophosphatidic acid receptor 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
Model detailsa receptor
AuthorsTaniguchi, R. / Nishizawa, T. / Ishitani, R. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
AMED-CREST Japan
CitationJournal: Nature / Year: 2017
Title: Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6
Authors: Taniguchi, R. / Inoue, A. / Sayama, M. / Uwamizu, A. / Yamashita, K. / Hirata, K. / Yoshida, M. / Tanaka, Y. / Kato, H.E. / Nakada-Nakura, Y. / Otani, Y. / Nishizawa, T. / Doi, T. / Ohwada, ...Authors: Taniguchi, R. / Inoue, A. / Sayama, M. / Uwamizu, A. / Yamashita, K. / Hirata, K. / Yoshida, M. / Tanaka, Y. / Kato, H.E. / Nakada-Nakura, Y. / Otani, Y. / Nishizawa, T. / Doi, T. / Ohwada, T. / Ishitani, R. / Aoki, J. / Nureki, O.
History
DepositionJun 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophosphatidic acid receptor 6a,Endolysin,Lysophosphatidic acid receptor 6a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4554
Polymers54,3861
Non-polymers1,0703
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.880, 65.020, 160.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysophosphatidic acid receptor 6a,Endolysin,Lysophosphatidic acid receptor 6a / Zgc:153784 / Zgc:153784 protein / Lysis protein / Lysozyme / Muramidase


Mass: 54385.574 Da / Num. of mol.: 1 / Mutation: E1011N,R1012G,D1020N,C1054T,C1097A,I1137R
Source method: isolated from a genetically manipulated source
Details: Chimera protein of UNP residues 1-227 from Lysophosphatidic acid receptor 6a (Q08BG4), UNP residues 2-161 from Endolysin (P00720),UNP residues 233-312 from Lysophosphatidic acid receptor 6a (Q08BG4).
Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: lpar6a, lpar6, zgc:153784 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08BG4, UniProt: P00720, lysozyme
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6 / Details: MES, PEG 400, NaH2PO4, 1,4-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→45.872 Å / Num. obs: 10233 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 32.72 % / Biso Wilson estimate: 83.51 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.56 / Rrim(I) all: 0.568 / Χ2: 1.342 / Net I/σ(I): 6.24 / Num. measured all: 334825 / Scaling rejects: 323
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.3931.9823.5650.6815820.5883.622100
3.39-3.6333.2241.7041.4715720.8451.73100
3.63-3.9233.411.0442.714120.8941.06100
3.92-4.2934.6050.7094.6413100.9330.719100
4.29-4.833.9440.5417.5411970.9630.55100
4.8-5.5432.7080.4578.9110640.9740.465100
5.54-6.7829.290.4318.789140.9710.438100
6.78-9.5631.9130.26118.457390.9930.265100
9.56-45.87230.9440.19523.394430.9960.19898

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNV and 2RH1

4xnv

2rh1


Resolution: 3.2→45.872 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.35
RfactorNum. reflection% reflection
Rfree0.2629 505 4.96 %
Rwork0.2358 --
obs0.2371 10188 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.78 Å2 / Biso mean: 67.7716 Å2 / Biso min: 34.82 Å2
Refinement stepCycle: final / Resolution: 3.2→45.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 41 0 3418
Biso mean--69.72 --
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083503
X-RAY DIFFRACTIONf_angle_d0.6574772
X-RAY DIFFRACTIONf_chiral_restr0.04579
X-RAY DIFFRACTIONf_plane_restr0.005592
X-RAY DIFFRACTIONf_dihedral_angle_d14.9832049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2-3.5220.31921230.291123582481
3.522-4.03130.28391260.235523922518
4.0313-5.0780.23871250.209824062531
5.078-45.87640.25321310.239425272658

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