4OC9 | pdb_00004oc9

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

• PDB DOI: https://doi.org/10.2210/pdb4OC9/pdb

• Classification: LYASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-08 Released: 2014-03-12 
• Deposition Author(s): Halavaty, A.S., Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

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

Halavaty, A.S., Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 754.7 kDa 
• Atom Count: 55,287 
• Modeled Residue Count: 6,624 
• Deposited Residue Count: 6,784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative O-acetylhomoserine (Thiol)-lyase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	424	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: Cj1727c, metB, metY EC: 2.5.1.49
UniProt
Find proteins for Q0P7Q4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P7Q4  Go to UniProtKB:  Q0P7Q4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	T [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	R [auth A], S [auth B], V [auth O]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	Q [auth A], U [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34oc9

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.434	α = 100.58
b = 149.787	β = 92.47
c = 186.591	γ = 90.1

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Halavaty, A.S., Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary