Structure of IDP90854

2.35 Angstrom resolution crystal structure of putative O-acetylhomoserine (thiol)-lyase (metY) from Campylobacter jejuni subsp. jejuni NCTC 11168 with N''''-Pyridoxyl-Lysine-5''''-Monophosphate at position 205

Edit deposit information
CSGID target
IDP90854 
PDB Id
4OC9 (NCBI MMDB
Authors
A.S.Halavaty,J.S.Brunzelle,Z.Wawrzak,O.Onopriyenko,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jan 08, 2014 
Release Date
Mar 12, 2014 

Annotation

Description
The crystal structure of the full-length putative O-acetylhomoserine (thiol)-lyase (metY) from Campylobacter jejuni subsp. jejuni NCTC 11168 with N''-Pyridoxyl-Lysine-5''-Monophosphate at position 205 was determined by single anomalous dispersion method and refined to 2.35 A resolution. There are 16 independent copies of the protein within the P1 asymmetric unit that are arranged in 4 tetramers with a total buried surface are of about 21000 A2 each. Individual chains interact via hydrogen and van der Waals contact. All chains are superimposable with an average 0.1 A r.m.s.d. over 420 C-alpha atoms. Each subunit consists of two domains that span residues 1–286, an N-terminal domain, and residues 287–423, a C-terminal domain. Lys205 of each protein chain is covalently modified with N''''''''''''''''''''''''''''''''-pyridoxyl-Lysine-5''''''''''''''''''''''''''''''''-monophosphate that is buried at the interface of the two domains and two subunits in a head-to-tail dimer; residues from each monomer coordinate the phosphate group of the ligand.  
Functional assignment
Lyase 

Ligands

Ligand code Name Ligand type
LLP biological
PO4 PHOSPHATE ION crystallization
IMD crystallization
GOL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=60.43Å, b=149.79Å, c=186.59Å
α=100.58, β=92.47, γ=90.10 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.65-2.35Å (2.41-2.35Å)  
Rall(%)
20.5 
Rwork(%)
20.2 (24.5) 
Rfree(%)
24.9 (32.6) 
Num. observed reflections
196428 (10604) 
Num. Rfree reflections
9821 (548) 
Completeness(%)
73.4 (53.5) 

Model parameters

Num Atoms
51662  
Num Waters
2983  
Num Hetatoms
3625  
Model mean isotropic B factor
24.150Å2  
RMSD bond length
0.012Å  
RMSD bond angle
2.009°  
Filename uploaded
4OC9.pdb (uploaded on Jun 04, 2015 4:27 PM)  
Inserted
Jan 08, 2014