6M34

Structural and functional insights into an Archaeal synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes

Wei, C.Sixue, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Digeranylgeranylglyceryl phosphate synthaseA, B283Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ0279
EC: 2.5.1.42
Membrane Entity: Yes 
UniProt
Find proteins for Q57727 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57727 
Go to UniProtKB:  Q57727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57727
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPG (Subject of Investigation/LOI)
Query on MPG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
I [auth B],
K [auth B]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
DMA (Subject of Investigation/LOI)
Query on DMA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
 Ligand Interaction
LDA (Subject of Investigation/LOI)
Query on LDA

Download Ideal Coordinates CCD File 
J [auth B]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.5α = 90
b = 79.75β = 111.87
c = 70.3γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PDB_EXTRACTdata extraction
HKL-2000data collection
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release