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- PDB-5xj8: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -

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Basic information

Entry
Database: PDB / ID: 5xj8
TitleCrystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the lysphosphatidic acid form
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / 1-hexadecanoyl-sn-glycero-3-phosphate / 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphate / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / LPA / lysophophatidic acid / lyso PA / lysoPA / 16:0 lyso PA / monoacylglycerol / palmitoyl lysophosphatidic acid / PA(16:0/0:0) / phospholipid biosynthesis / PlsY / YgiH
Function / homology
Function and homology information


acyl phosphate:glycerol-3-phosphate acyltransferase / acyl-phosphate glycerol-3-phosphate acyltransferase activity / phospholipid biosynthetic process / plasma membrane
Similarity search - Function
Glycerol-3-phosphate acyltransferase, PlsY / Glycerol-3-phosphate acyltransferase / Glycerol-3-phosphate acyltransferase
Similarity search - Domain/homology
Chem-NKO / PHOSPHATE ION / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsLi, Z. / Tang, Y. / Li, D.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570748 China
National Natural Science Foundation of ChinaU1632127 China
Chinese Academy of Sciences (CAS)-Shanghai Science Research CenterCAS-SSRC-YJ-2015-02 China
Key Program of CAS Frontier ScienceQYZDB-SSW-SMC037 China
1000 Young Talent Program2015 China
Shanghai Pujiang Talent Program15PJ1409400 China
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the committed step of bacterial phospholipid biosynthesis.
Authors: Li, Z. / Tang, Y. / Wu, Y. / Zhao, S. / Bao, J. / Luo, Y. / Li, D.
History
DepositionApr 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol-3-phosphate acyltransferase
B: Glycerol-3-phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4796
Polymers43,7842
Non-polymers6954
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-35 kcal/mol
Surface area18470 Å2
Unit cell
Length a, b, c (Å)123.888, 40.895, 91.705
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycerol-3-phosphate acyltransferase / Acyl-PO4 G3P acyltransferase / Acyl-phosphate--glycerol-3-phosphate acyltransferase / G3P ...Acyl-PO4 G3P acyltransferase / Acyl-phosphate--glycerol-3-phosphate acyltransferase / G3P acyltransferase / GPAT / Lysophosphatidic acid synthase / LPA synthase


Mass: 21892.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: plsY, aq_676 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66905, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NKO / (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate / 16:0 LPA / palmitoyl lysophosphatidic acid


Mass: 410.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H39O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 1mol% of palmitoyl lysophosphatidic acid, 39% PEG 350 MME, 0.04M NaCl, 0.04M Tris HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.41→35.33 Å / Num. obs: 18124 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Net I/σ(I): 11.37
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.448 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→35.33 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2635 890 5 %
Rwork0.2283 --
obs0.23 17801 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.41→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 42 17 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023181
X-RAY DIFFRACTIONf_angle_d0.4594316
X-RAY DIFFRACTIONf_dihedral_angle_d8.7652399
X-RAY DIFFRACTIONf_chiral_restr0.034504
X-RAY DIFFRACTIONf_plane_restr0.002516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4059-2.55660.32011350.28882707X-RAY DIFFRACTION96
2.5566-2.75390.28841490.24182773X-RAY DIFFRACTION99
2.7539-3.03090.27741620.23522794X-RAY DIFFRACTION99
3.0309-3.46910.27791550.23352839X-RAY DIFFRACTION99
3.4691-4.36940.27271390.21552866X-RAY DIFFRACTION99
4.3694-35.33540.22941500.21692932X-RAY DIFFRACTION99

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