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- PDB-5xj7: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -

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Basic information

Entry
Database: PDB / ID: 5xj7
TitleCrystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the acyl phosphate form
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / 16:0-P / acylP / acyl phosphate / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / monoacylglycerol / phospholipid biosynthesis / substrate / palmitoyl phosphate / 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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / phosphono hexadecanoate / : / PHOSPHATE ION / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsTang, Y. / Li, Z. / 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 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,93913
Polymers21,8921
Non-polymers3,04712
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-9 kcal/mol
Surface area9690 Å2
Unit cell
Length a, b, c (Å)46.224, 65.599, 84.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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

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Non-polymers , 5 types, 65 molecules

#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-87O / phosphono hexadecanoate


Mass: 336.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H33O5P
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 8
Details: 7.8 monoacylglycerol (7.8 MAG), 0.6M potassium fluoride, 22-26% PEG 400, 0.1M Tris HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.77→46.22 Å / Num. obs: 25689 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Net I/σ(I): 18
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.429 / % possible all: 97.1

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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: 1.772→40.573 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.2254 1337 5.29 %
Rwork0.1953 --
obs0.1969 25262 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.772→40.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 205 53 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061766
X-RAY DIFFRACTIONf_angle_d0.9732350
X-RAY DIFFRACTIONf_dihedral_angle_d11.1791337
X-RAY DIFFRACTIONf_chiral_restr0.045258
X-RAY DIFFRACTIONf_plane_restr0.005274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7725-1.83580.35491450.31962297X-RAY DIFFRACTION97
1.8358-1.90930.26221320.24622355X-RAY DIFFRACTION99
1.9093-1.99620.24441350.21632357X-RAY DIFFRACTION99
1.9962-2.10140.23461220.18262379X-RAY DIFFRACTION98
2.1014-2.23310.22051280.17262350X-RAY DIFFRACTION98
2.2331-2.40550.20521340.17782373X-RAY DIFFRACTION99
2.4055-2.64750.24661350.16672400X-RAY DIFFRACTION99
2.6475-3.03050.18851070.17222430X-RAY DIFFRACTION98
3.0305-3.81770.18911510.17892443X-RAY DIFFRACTION99
3.8177-40.58320.24031480.21412541X-RAY DIFFRACTION98

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