[English] 日本語
Yorodumi
- PDB-6m31: Structural and Functional Insights into an Archaeal Lipid Synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m31
TitleStructural and Functional Insights into an Archaeal Lipid Synthase
ComponentsDigeranylgeranylglyceryl phosphate synthase
KeywordsMEMBRANE PROTEIN / Lipid
Function / homology
Function and homology information


geranylgeranylglycerol-phosphate geranylgeranyltransferase / geranylgeranylglycerol-phosphate geranylgeranyltransferase activity / glycerophospholipid metabolic process / phospholipid biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Digeranylgeranylglyceryl phosphate synthase / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family
Similarity search - Domain/homology
Chem-MPG / PHOSPHATE ION / Digeranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsRen, S. / Cheng, W.
CitationJournal: Cell Rep / Year: 2020
Title: Structural and Functional Insights into an Archaeal Lipid Synthase
Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / ...Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / Zhang, W. / Li, W. / Wei, Y. / Driessen, A.J. / Cheng, W.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Aug 17, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Digeranylgeranylglyceryl phosphate synthase
B: Digeranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,78950
Polymers63,5712
Non-polymers12,21748
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25390 Å2
ΔGint52 kcal/mol
Surface area28890 Å2
Unit cell
Length a, b, c (Å)70.000, 133.490, 79.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Digeranylgeranylglyceryl phosphate synthase / DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol- ...DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol-phosphate geranylgeranyltransferase


Mass: 31785.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ0279 / Production host: Escherichia coli ATCC 8739 (bacteria) / Strain (production host): ATCC 8739
References: UniProt: Q57727, geranylgeranylglycerol-phosphate geranylgeranyltransferase

-
Non-polymers , 5 types, 91 molecules

#2: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 200 mM NaCl, 20% (w/v) PEG500, and 200 mM Tris-HCl (pH 8.0).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→48.89 Å / Num. obs: 33780 / % possible obs: 99.8 % / Redundancy: 6.904 % / Biso Wilson estimate: 45.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Χ2: 1.221 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.29-2.436.9740.7732.63102850.930.83499.5
2.43-2.66.7130.5243.7696820.9620.56899.8
2.6-2.817.1910.3475.7790290.9870.37499.8
2.81-3.086.8690.2188.5383140.9930.23699.9
3.08-3.446.9660.12213.5775320.9970.13299.9
3.44-3.976.9620.07266180.9990.078100

-
Processing

Software
NameVersionClassification
SHELXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1689 5 %RANDOM
Rwork0.201 ---
obs0.202 33780 99.8 %-
Displacement parametersBiso max: 145.39 Å2 / Biso mean: 54.73 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-8.2408 Å20 Å20 Å2
2---15.7522 Å20 Å2
3---7.5114 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.3→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 845 43 5336
Biso mean--80.86 55.6 -
Num. residues----560
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3206 34 5.03 %
Rwork0.2379 642 -
all0.2419 676 -
obs--99.42 %

+
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://pdbjlvh1.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