6E6I

Crystal structure of 4-methyl HOPDA bound to LigY from Sphingobium sp. strain SYK-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies

Kuatsjah, E.Chan, A.C.K.Hurst, T.E.Snieckus, V.Murphy, M.E.P.Eltis, L.D.

(2018) Acs Catalysis 8: 11622-11632


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, D, E, F, G, H, I
332Sphingobium 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, D, E, F, G, H, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HVS
Query on HVS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
(1Z,3E)-5-carboxy-3-methyl-5-oxo-1-phenylpenta-1,3-dien-1-olate
C13 H11 O4
JCSKQBIZFFCCKU-UVTPKQPNSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 180.645α = 90.00
b = 195.099β = 90.00
c = 179.917γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada04802
Natural Sciences and Engineering Research Council (Canada)Canada171359

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release