5VN5

Crystal structure of LigY from Sphingobium sp. strain SYK-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The bacterialmeta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha / beta-hydrolase superfamily.

Kuatsjah, E.Chan, A.C.K.Kobylarz, M.J.Murphy, M.E.P.Eltis, L.D.

(2017) J. Biol. Chem. 292: 18290-18302


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
A, B, C
338Sphingobium sp. (strain NBRC 103272 / SYK-6)Mutation(s): 0 
Gene Names: ligY
Find proteins for G2IN02 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Go to UniProtKB:  G2IN02
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 60.020α = 90.00
b = 195.361β = 90.00
c = 178.249γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Genome CanadaCanada2108
Natural Sciences and Engineering Research Council (Canada)Canada171359

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references