6HY3

Three-dimensional structure of AgaC from Zobellia galactanivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The agar-specific hydrolaseZgAgaC from the marine bacteriumZobellia galactanivoransdefines a new GH16 protein subfamily.

Naretto, A.Fanuel, M.Ropartz, D.Rogniaux, H.Larocque, R.Czjzek, M.Tellier, C.Michel, G.

(2019) J.Biol.Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-agarase C
A
272Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)Mutation(s): 0 
Gene Names: agaC
EC: 3.2.1.81
Find proteins for D7GXG5 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Go to UniProtKB:  D7GXG5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.604α = 90.00
b = 101.498β = 90.00
c = 46.693γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MoRDaphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Database references