[English] 日本語
Yorodumi
- PDB-5xj9: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xj9
TitleCrystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the orthophosphate form
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / monoacylglycerol / phosphate / product / 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 / PHOSPHATE ION / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,88314
Polymers21,8921
Non-polymers2,99113
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-34 kcal/mol
Surface area10210 Å2
Unit cell
Length a, b, c (Å)58.339, 97.986, 83.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

-
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.: 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)
References: UniProt: O66905, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H34O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 7
Details: 1 mol% palmitoyl lysophosphatidic acid, 0.4 M Na2HPO4, 24% PEG 400, 0.1M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.83→31.73 Å / Num. obs: 21613 / % possible obs: 95.35 % / Redundancy: 6 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.075 / Net I/σ(I): 7.02
Reflection shellResolution: 1.83→1.89 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.28 / Rpim(I) all: 0.433 / % possible all: 86.02

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→31.73 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.25 2001 9.74 %
Rwork0.2055 --
obs0.2099 20554 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 201 104 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071802
X-RAY DIFFRACTIONf_angle_d0.862404
X-RAY DIFFRACTIONf_dihedral_angle_d11.3281366
X-RAY DIFFRACTIONf_chiral_restr0.045268
X-RAY DIFFRACTIONf_plane_restr0.005283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87050.40481210.41531085X-RAY DIFFRACTION80
1.8705-1.9210.43131380.38621259X-RAY DIFFRACTION91
1.921-1.97760.3891340.32091287X-RAY DIFFRACTION94
1.9776-2.04140.33641380.28911275X-RAY DIFFRACTION93
2.0414-2.11430.35341400.24311311X-RAY DIFFRACTION95
2.1143-2.1990.31041430.22971322X-RAY DIFFRACTION96
2.199-2.2990.2551400.19731313X-RAY DIFFRACTION96
2.299-2.42020.2551470.19371336X-RAY DIFFRACTION96
2.4202-2.57180.24541480.1731347X-RAY DIFFRACTION97
2.5718-2.77020.20771410.17391352X-RAY DIFFRACTION97
2.7702-3.04880.22061480.16671381X-RAY DIFFRACTION98
3.0488-3.48950.20241540.16691385X-RAY DIFFRACTION99
3.4895-4.39460.19061500.16671425X-RAY DIFFRACTION99
4.3946-31.730.21171590.18821475X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more