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 | PYRIDOXAL-5''-PHOSPHATE | biological |
| PO4 | crystallization | |
| IMD | crystallization | |
| GOL | glycerol | 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
- 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)
- 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