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- PDB-5xj5: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -

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Basic information

Entry
Database: PDB / ID: 5xj5
TitleCrystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the monoacylglycerol form
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / glycerol 3-phosphate acyltransferase / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / monoacylglycerol / 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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / GLYCINE / TRIETHYLENE GLYCOL / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.481 Å
AuthorsLi, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,50725
Polymers21,8921
Non-polymers5,61524
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.675, 83.437, 107.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 / Plasmid: p3EG
Details (production host): pET backbone with eGFP fusion at C terminal
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, 97 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 3.8
Details: 7.8 monoacylglycerol (7.8 MAG), 0.1 M ammonium sulphate, 25-30% triethylene glycole, 0.1 M glycine/HCl pH 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.48→47.44 Å / Num. obs: 43520 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Net I/σ(I): 16.6
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.428 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.481→35.582 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2111 4.94 %Random selection
Rwork0.1877 ---
obs0.1889 42709 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.481→35.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 380 73 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061959
X-RAY DIFFRACTIONf_angle_d0.8982564
X-RAY DIFFRACTIONf_dihedral_angle_d14.2911126
X-RAY DIFFRACTIONf_chiral_restr0.064272
X-RAY DIFFRACTIONf_plane_restr0.005296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4807-1.51520.31691360.28452513X-RAY DIFFRACTION93
1.5152-1.5530.26211260.25682636X-RAY DIFFRACTION97
1.553-1.5950.29351250.24352675X-RAY DIFFRACTION98
1.595-1.6420.24571510.22922688X-RAY DIFFRACTION98
1.642-1.6950.23571330.22022673X-RAY DIFFRACTION98
1.695-1.75550.25241380.21042683X-RAY DIFFRACTION98
1.7555-1.82580.2351420.19662674X-RAY DIFFRACTION99
1.8258-1.90890.22261310.18472728X-RAY DIFFRACTION99
1.9089-2.00960.20441270.18212711X-RAY DIFFRACTION98
2.0096-2.13550.21441360.17232675X-RAY DIFFRACTION97
2.1355-2.30030.17581570.16932728X-RAY DIFFRACTION99
2.3003-2.53170.17571440.16632771X-RAY DIFFRACTION100
2.5317-2.89790.18061410.16072779X-RAY DIFFRACTION100
2.8979-3.65050.2261550.17642780X-RAY DIFFRACTION99
3.6505-35.59240.21431690.19792884X-RAY DIFFRACTION99

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