PDB-4oc9: 2.35 Angstrom resolution crystal structure of putative O-acetylho...

Basic information

• Entry: Database: PDB / ID: 4oc9
• Title: 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
• Components: Putative O-acetylhomoserine (Thiol)-lyase
• Keywords: LYASE / O-acetylhomoserine (thiol)-lyase / PLP-dependent enzymes / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Function:

O-acetylhomoserine aminocarboxypropyltransferase / O-acetylhomoserine aminocarboxypropyltransferase activity / L-homocysteine biosynthetic process / cysteine synthase activity / transsulfuration / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm

Domain/homology:

O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta

Component:

IMIDAZOLE / PHOSPHATE ION / O-acetylhomoserine (Thiol)-lyase

• Biological species: Campylobacter jejuni (Campylobacter)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
• Authors: Halavaty, A.S. / Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
• Citation: Journal: To be Published; Title: 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; Authors: Halavaty, A.S. / Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 8, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2014	Group: Other
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Mar 26, 2025	Group: Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Putative O-acetylhomoserine (Thiol)-lyase

B: Putative O-acetylhomoserine (Thiol)-lyase

C: Putative O-acetylhomoserine (Thiol)-lyase

D: Putative O-acetylhomoserine (Thiol)-lyase

E: Putative O-acetylhomoserine (Thiol)-lyase

F: Putative O-acetylhomoserine (Thiol)-lyase

G: Putative O-acetylhomoserine (Thiol)-lyase

H: Putative O-acetylhomoserine (Thiol)-lyase

I: Putative O-acetylhomoserine (Thiol)-lyase

J: Putative O-acetylhomoserine (Thiol)-lyase

K: Putative O-acetylhomoserine (Thiol)-lyase

L: Putative O-acetylhomoserine (Thiol)-lyase

M: Putative O-acetylhomoserine (Thiol)-lyase

N: Putative O-acetylhomoserine (Thiol)-lyase

O: Putative O-acetylhomoserine (Thiol)-lyase

P: Putative O-acetylhomoserine (Thiol)-lyase

hetero molecules

Summary:

• 755 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	754,695	22
Polymers	754,186	16
Non-polymers	509	6
Water	53,739	2983

1

A: Putative O-acetylhomoserine (Thiol)-lyase

D: Putative O-acetylhomoserine (Thiol)-lyase

M: Putative O-acetylhomoserine (Thiol)-lyase

N: Putative O-acetylhomoserine (Thiol)-lyase

hetero molecules

Summary:

• defined by author&software
• 189 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	188,777	7
Polymers	188,546	4
Non-polymers	230	3
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	21440 Å2
ΔGint	-113 kcal/mol
Surface area	48540 Å2
Method	PISA

2

B: Putative O-acetylhomoserine (Thiol)-lyase

C: Putative O-acetylhomoserine (Thiol)-lyase

O: Putative O-acetylhomoserine (Thiol)-lyase

P: Putative O-acetylhomoserine (Thiol)-lyase

hetero molecules

Summary:

• defined by author&software
• 189 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	188,826	7
Polymers	188,546	4
Non-polymers	279	3
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	21350 Å2
ΔGint	-121 kcal/mol
Surface area	49140 Å2
Method	PISA

3

E: Putative O-acetylhomoserine (Thiol)-lyase

F: Putative O-acetylhomoserine (Thiol)-lyase

K: Putative O-acetylhomoserine (Thiol)-lyase

L: Putative O-acetylhomoserine (Thiol)-lyase

Summary:

• defined by author&software
• 189 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	188,546	4
Polymers	188,546	4
Non-polymers	0	0
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	20780 Å2
ΔGint	-116 kcal/mol
Surface area	48800 Å2
Method	PISA

4

G: Putative O-acetylhomoserine (Thiol)-lyase

H: Putative O-acetylhomoserine (Thiol)-lyase

I: Putative O-acetylhomoserine (Thiol)-lyase

J: Putative O-acetylhomoserine (Thiol)-lyase

Summary:

• defined by author&software
• 189 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	188,546	4
Polymers	188,546	4
Non-polymers	0	0
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	20740 Å2
ΔGint	-117 kcal/mol
Surface area	48780 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	60.434, 149.787, 186.591
Angle α, β, γ (deg.)	100.58, 92.47, 90.10
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	A
2	12	M
1	13	A
2	13	N
1	14	A
2	14	O
1	15	A
2	15	P
1	16	B
2	16	C
1	17	B
2	17	D
1	18	B
2	18	E
1	19	B
2	19	F
1	20	B
2	20	G
1	21	B
2	21	H
1	22	B
2	22	I
1	23	B
2	23	J
1	24	B
2	24	K
1	25	B
2	25	L
1	26	B
2	26	M
1	27	B
2	27	N
1	28	B
2	28	O
1	29	B
2	29	P
1	30	C
2	30	D
1	31	C
2	31	E
1	32	C
2	32	F
1	33	C
2	33	G
1	34	C
2	34	H
1	35	C
2	35	I
1	36	C
2	36	J
1	37	C
2	37	K
1	38	C
2	38	L
1	39	C
2	39	M
1	40	C
2	40	N
1	41	C
2	41	O
1	42	C
2	42	P
1	43	D
2	43	E
1	44	D
2	44	F
1	45	D
2	45	G
1	46	D
2	46	H
1	47	D
2	47	I
1	48	D
2	48	J
1	49	D
2	49	K
1	50	D
2	50	L
1	51	D
2	51	M
1	52	D
2	52	N
1	53	D
2	53	O
1	54	D
2	54	P
1	55	E
2	55	F
1	56	E
2	56	G
1	57	E
2	57	H
1	58	E
2	58	I
1	59	E
2	59	J
1	60	E
2	60	K
1	61	E
2	61	L
1	62	E
2	62	M
1	63	E
2	63	N
1	64	E
2	64	O
1	65	E
2	65	P
1	66	F
2	66	G
1	67	F
2	67	H
1	68	F
2	68	I
1	69	F
2	69	J
1	70	F
2	70	K
1	71	F
2	71	L
1	72	F
2	72	M
1	73	F
2	73	N
1	74	F
2	74	O
1	75	F
2	75	P
1	76	G
2	76	H
1	77	G
2	77	I
1	78	G
2	78	J
1	79	G
2	79	K
1	80	G
2	80	L
1	81	G
2	81	M
1	82	G
2	82	N
1	83	G
2	83	O
1	84	G
2	84	P
1	85	H
2	85	I
1	86	H
2	86	J
1	87	H
2	87	K
1	88	H
2	88	L
1	89	H
2	89	M
1	90	H
2	90	N
1	91	H
2	91	O
1	92	H
2	92	P
1	93	I
2	93	J
1	94	I
2	94	K
1	95	I
2	95	L
1	96	I
2	96	M
1	97	I
2	97	N
1	98	I
2	98	O
1	99	I
2	99	P
1	100	J
2	100	K
1	101	J
2	101	L
1	102	J
2	102	M
1	103	J
2	103	N
1	104	J
2	104	O
1	105	J
2	105	P
1	106	K
2	106	L
1	107	K
2	107	M
1	108	K
2	108	N
1	109	K
2	109	O
1	110	K
2	110	P
1	111	L
2	111	M
1	112	L
2	112	N
1	113	L
2	113	O
1	114	L
2	114	P
1	115	M
2	115	N
1	116	M
2	116	O
1	117	M
2	117	P
1	118	N
2	118	O
1	119	N
2	119	P
1	120	O
2	120	P

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	1	PHE	PHE	SER	SER	B	B	3 - 423	4 - 424
1	2	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	2	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
1	3	PHE	PHE	GLU	GLU	A	A	3 - 422	4 - 423
2	3	PHE	PHE	GLU	GLU	D	D	3 - 422	4 - 423
1	4	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	4	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
1	5	PHE	PHE	GLU	GLU	A	A	3 - 422	4 - 423
2	5	PHE	PHE	GLU	GLU	F	F	3 - 422	4 - 423
1	6	PHE	PHE	GLU	GLU	A	A	3 - 422	4 - 423
2	6	PHE	PHE	GLU	GLU	G	G	3 - 422	4 - 423
1	7	PHE	PHE	GLU	GLU	A	A	3 - 422	4 - 423
2	7	PHE	PHE	GLU	GLU	H	H	3 - 422	4 - 423
1	8	PHE	PHE	GLU	GLU	A	A	3 - 422	4 - 423
2	8	PHE	PHE	GLU	GLU	I	I	3 - 422	4 - 423
1	9	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	9	PHE	PHE	SER	SER	J	J	3 - 423	4 - 424
1	10	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	10	PHE	PHE	SER	SER	K	K	3 - 423	4 - 424
1	11	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	11	PHE	PHE	SER	SER	L	L	3 - 423	4 - 424
1	12	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	12	PHE	PHE	SER	SER	M	M	3 - 423	4 - 424
1	13	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	13	PHE	PHE	SER	SER	N	N	3 - 423	4 - 424
1	14	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	14	PHE	PHE	SER	SER	O	O	3 - 423	4 - 424
1	15	PHE	PHE	SER	SER	A	A	3 - 423	4 - 424
2	15	PHE	PHE	SER	SER	P	P	3 - 423	4 - 424
1	16	PHE	PHE	SER	SER	B	B	3 - 423	4 - 424
2	16	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
1	17	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	17	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
1	18	PHE	PHE	SER	SER	B	B	3 - 423	4 - 424
2	18	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
1	19	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	19	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
1	20	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	20	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
1	21	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	21	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
1	22	ASN	ASN	GLU	GLU	B	B	2 - 422	3 - 423
2	22	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
1	23	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	23	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
1	24	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	24	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	25	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	25	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	26	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	26	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	27	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	27	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	28	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	28	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	29	ASN	ASN	SER	SER	B	B	2 - 423	3 - 424
2	29	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	30	PHE	PHE	GLU	GLU	C	C	3 - 422	4 - 423
2	30	PHE	PHE	GLU	GLU	D	D	3 - 422	4 - 423
1	31	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	31	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
1	32	PHE	PHE	GLU	GLU	C	C	3 - 422	4 - 423
2	32	PHE	PHE	GLU	GLU	F	F	3 - 422	4 - 423
1	33	PHE	PHE	GLU	GLU	C	C	3 - 422	4 - 423
2	33	PHE	PHE	GLU	GLU	G	G	3 - 422	4 - 423
1	34	PHE	PHE	GLU	GLU	C	C	3 - 422	4 - 423
2	34	PHE	PHE	GLU	GLU	H	H	3 - 422	4 - 423
1	35	PHE	PHE	GLU	GLU	C	C	3 - 422	4 - 423
2	35	PHE	PHE	GLU	GLU	I	I	3 - 422	4 - 423
1	36	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	36	PHE	PHE	SER	SER	J	J	3 - 423	4 - 424
1	37	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	37	PHE	PHE	SER	SER	K	K	3 - 423	4 - 424
1	38	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	38	PHE	PHE	SER	SER	L	L	3 - 423	4 - 424
1	39	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	39	PHE	PHE	SER	SER	M	M	3 - 423	4 - 424
1	40	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	40	PHE	PHE	SER	SER	N	N	3 - 423	4 - 424
1	41	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	41	PHE	PHE	SER	SER	O	O	3 - 423	4 - 424
1	42	PHE	PHE	SER	SER	C	C	3 - 423	4 - 424
2	42	PHE	PHE	SER	SER	P	P	3 - 423	4 - 424
1	43	PHE	PHE	GLU	GLU	D	D	3 - 422	4 - 423
2	43	PHE	PHE	GLU	GLU	E	E	3 - 422	4 - 423
1	44	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	44	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
1	45	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	45	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
1	46	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	46	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
1	47	ASN	ASN	GLU	GLU	D	D	2 - 422	3 - 423
2	47	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
1	48	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	48	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
1	49	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	49	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	50	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	50	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	51	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	51	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	52	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	52	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	53	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	53	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	54	ASN	ASN	SER	SER	D	D	2 - 423	3 - 424
2	54	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	55	PHE	PHE	GLU	GLU	E	E	3 - 422	4 - 423
2	55	PHE	PHE	GLU	GLU	F	F	3 - 422	4 - 423
1	56	PHE	PHE	GLU	GLU	E	E	3 - 422	4 - 423
2	56	PHE	PHE	GLU	GLU	G	G	3 - 422	4 - 423
1	57	PHE	PHE	GLU	GLU	E	E	3 - 422	4 - 423
2	57	PHE	PHE	GLU	GLU	H	H	3 - 422	4 - 423
1	58	PHE	PHE	GLU	GLU	E	E	3 - 422	4 - 423
2	58	PHE	PHE	GLU	GLU	I	I	3 - 422	4 - 423
1	59	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	59	PHE	PHE	SER	SER	J	J	3 - 423	4 - 424
1	60	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	60	PHE	PHE	SER	SER	K	K	3 - 423	4 - 424
1	61	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	61	PHE	PHE	SER	SER	L	L	3 - 423	4 - 424
1	62	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	62	PHE	PHE	SER	SER	M	M	3 - 423	4 - 424
1	63	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	63	PHE	PHE	SER	SER	N	N	3 - 423	4 - 424
1	64	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	64	PHE	PHE	SER	SER	O	O	3 - 423	4 - 424
1	65	PHE	PHE	SER	SER	E	E	3 - 423	4 - 424
2	65	PHE	PHE	SER	SER	P	P	3 - 423	4 - 424
1	66	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	66	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
1	67	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	67	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
1	68	ASN	ASN	GLU	GLU	F	F	2 - 422	3 - 423
2	68	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
1	69	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	69	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
1	70	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	70	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	71	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	71	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	72	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	72	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	73	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	73	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	74	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	74	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	75	ASN	ASN	SER	SER	F	F	2 - 423	3 - 424
2	75	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	76	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	76	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
1	77	ASN	ASN	GLU	GLU	G	G	2 - 422	3 - 423
2	77	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
1	78	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	78	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
1	79	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	79	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	80	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	80	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	81	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	81	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	82	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	82	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	83	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	83	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	84	ASN	ASN	SER	SER	G	G	2 - 423	3 - 424
2	84	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	85	ASN	ASN	GLU	GLU	H	H	2 - 422	3 - 423
2	85	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
1	86	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	86	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
1	87	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	87	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	88	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	88	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	89	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	89	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	90	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	90	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	91	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	91	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	92	ASN	ASN	SER	SER	H	H	2 - 423	3 - 424
2	92	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	93	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	93	ASN	ASN	GLU	GLU	J	J	2 - 422	3 - 423
1	94	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	94	ASN	ASN	GLU	GLU	K	K	2 - 422	3 - 423
1	95	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	95	ASN	ASN	GLU	GLU	L	L	2 - 422	3 - 423
1	96	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	96	ASN	ASN	GLU	GLU	M	M	2 - 422	3 - 423
1	97	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	97	ASN	ASN	GLU	GLU	N	N	2 - 422	3 - 423
1	98	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	98	ASN	ASN	GLU	GLU	O	O	2 - 422	3 - 423
1	99	ASN	ASN	GLU	GLU	I	I	2 - 422	3 - 423
2	99	ASN	ASN	GLU	GLU	P	P	2 - 422	3 - 423
1	100	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	100	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
1	101	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	101	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	102	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	102	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	103	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	103	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	104	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	104	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	105	ASN	ASN	SER	SER	J	J	2 - 423	3 - 424
2	105	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	106	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
2	106	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
1	107	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
2	107	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	108	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
2	108	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	109	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
2	109	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	110	ASN	ASN	SER	SER	K	K	2 - 423	3 - 424
2	110	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	111	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
2	111	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
1	112	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
2	112	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	113	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
2	113	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	114	ASN	ASN	SER	SER	L	L	2 - 423	3 - 424
2	114	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	115	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
2	115	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
1	116	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
2	116	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	117	ASN	ASN	SER	SER	M	M	2 - 423	3 - 424
2	117	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	118	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
2	118	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
1	119	ASN	ASN	SER	SER	N	N	2 - 423	3 - 424
2	119	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424
1	120	ASN	ASN	SER	SER	O	O	2 - 423	3 - 424
2	120	ASN	ASN	SER	SER	P	P	2 - 423	3 - 424

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120

Components

#1: Protein

A B C D E F G H I J K L M N O P
Putative O-acetylhomoserine (Thiol)-lyase

Details:

Mass: 47136.605 Da / Num. of mol.: 16
Mutation: Lys205 modified by PYRIDOXAL-5'-PHOSPHATE to become N'-Pyridoxyl-Lysine-5'-Monophosphate
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj1727c, metB, metY / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q0P7Q4, O-acetylhomoserine aminocarboxypropyltransferase

#2: Chemical

A-501 D-501 ChemComp-IMD / IMIDAZOLE

Details:

Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂

#3: Chemical

A-502 B-501 O-501 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

C-501 ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 2983 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.2 ų/Da / Density % sol: 44.07 %
• Crystal grow: Temperature: 295 K / pH: 7.5 ; Details: protein: 1.85 mg/mL crystallization: 25%PEG 3350, 0.2M Mg Chloride, 0.1M Tris, cryo conditions: paraton, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
• Detector: Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 / Details: BE-LENSES
• Radiation: Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97856 Å / Relative weight: 1
• Reflection: Resolution: 2.35→30 Å / Num. obs: 255734 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 25.7 Ų / R_merge(I) obs: 0.113 / Net I/σ(I): 10.9
• Reflection shell: Resolution: 2.35→2.39 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.448 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6

Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
HKL-3000		phasing
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure: SAD / Resolution: 2.35→29.65 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.911 / SU B: 8.531 / SU ML: 0.204 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.249	9880	5 %	RANDOM
Rwork	0.202	-	-	-
obs	0.205	186548	73.4 %	-
all	-	186548	-	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 24.15 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.27 Å2	-0.16 Å2	-0.09 Å2
2-	-	-1.3 Å2	0.32 Å2
3-	-	-	0.92 Å2

Refinement step

Cycle: LAST / Resolution: 2.35→29.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	51922	0	33	2983	54938

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	53408
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	50978
X-RAY DIFFRACTION	r_angle_refined_deg	2.009	1.963	72522
X-RAY DIFFRACTION	r_angle_other_deg	1.559	3	117102
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.487	5	6695
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.572	25.28	2519
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.924	15	8932
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.305	15	209
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	8219
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	61721
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	12474
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	26913	0.06
1	2	B	26913	0.06
2	1	A	27030	0.06
2	2	C	27030	0.06
3	1	A	27051	0.06
3	2	D	27051	0.06
4	1	A	27079	0.06
4	2	E	27079	0.06
5	1	A	26947	0.06
5	2	F	26947	0.06
6	1	A	27068	0.05
6	2	G	27068	0.05
7	1	A	27203	0.05
7	2	H	27203	0.05
8	1	A	25651	0.07
8	2	I	25651	0.07
9	1	A	25970	0.06
9	2	J	25970	0.06
10	1	A	25760	0.07
10	2	K	25760	0.07
11	1	A	25885	0.07
11	2	L	25885	0.07
12	1	A	25914	0.06
12	2	M	25914	0.06
13	1	A	25833	0.07
13	2	N	25833	0.07
14	1	A	25795	0.07
14	2	O	25795	0.07
15	1	A	26204	0.06
15	2	P	26204	0.06
16	1	B	26827	0.07
16	2	C	26827	0.07
17	1	B	27126	0.06
17	2	D	27126	0.06
18	1	B	27203	0.06
18	2	E	27203	0.06
19	1	B	27002	0.07
19	2	F	27002	0.07
20	1	B	27012	0.06
20	2	G	27012	0.06
21	1	B	27163	0.05
21	2	H	27163	0.05
22	1	B	25894	0.07
22	2	I	25894	0.07
23	1	B	26074	0.06
23	2	J	26074	0.06
24	1	B	25866	0.07
24	2	K	25866	0.07
25	1	B	26034	0.07
25	2	L	26034	0.07
26	1	B	26266	0.07
26	2	M	26266	0.07
27	1	B	26016	0.07
27	2	N	26016	0.07
28	1	B	25933	0.07
28	2	O	25933	0.07
29	1	B	26297	0.07
29	2	P	26297	0.07
30	1	C	27118	0.05
30	2	D	27118	0.05
31	1	C	27145	0.05
31	2	E	27145	0.05
32	1	C	27141	0.05
32	2	F	27141	0.05
33	1	C	27093	0.05
33	2	G	27093	0.05
34	1	C	27137	0.05
34	2	H	27137	0.05
35	1	C	25727	0.06
35	2	I	25727	0.06
36	1	C	26046	0.06
36	2	J	26046	0.06
37	1	C	25894	0.07
37	2	K	25894	0.07
38	1	C	25928	0.07
38	2	L	25928	0.07
39	1	C	26051	0.06
39	2	M	26051	0.06
40	1	C	25942	0.06
40	2	N	25942	0.06
41	1	C	25902	0.07
41	2	O	25902	0.07
42	1	C	26308	0.06
42	2	P	26308	0.06
43	1	D	27165	0.05
43	2	E	27165	0.05
44	1	D	27121	0.06
44	2	F	27121	0.06
45	1	D	27173	0.06
45	2	G	27173	0.06
46	1	D	27316	0.05
46	2	H	27316	0.05
47	1	D	25811	0.06
47	2	I	25811	0.06
48	1	D	26118	0.06
48	2	J	26118	0.06
49	1	D	25972	0.06
49	2	K	25972	0.06
50	1	D	26149	0.06
50	2	L	26149	0.06
51	1	D	26153	0.06
51	2	M	26153	0.06
52	1	D	26118	0.06
52	2	N	26118	0.06
53	1	D	26056	0.06
53	2	O	26056	0.06
54	1	D	26428	0.06
54	2	P	26428	0.06
55	1	E	27049	0.06
55	2	F	27049	0.06
56	1	E	27116	0.06
56	2	G	27116	0.06
57	1	E	27212	0.05
57	2	H	27212	0.05
58	1	E	25770	0.06
58	2	I	25770	0.06
59	1	E	26137	0.06
59	2	J	26137	0.06
60	1	E	25894	0.06
60	2	K	25894	0.06
61	1	E	26015	0.07
61	2	L	26015	0.07
62	1	E	26112	0.06
62	2	M	26112	0.06
63	1	E	25976	0.07
63	2	N	25976	0.07
64	1	E	25925	0.07
64	2	O	25925	0.07
65	1	E	26404	0.06
65	2	P	26404	0.06
66	1	F	27029	0.06
66	2	G	27029	0.06
67	1	F	27186	0.05
67	2	H	27186	0.05
68	1	F	25749	0.07
68	2	I	25749	0.07
69	1	F	26017	0.06
69	2	J	26017	0.06
70	1	F	25773	0.07
70	2	K	25773	0.07
71	1	F	25893	0.07
71	2	L	25893	0.07
72	1	F	26066	0.07
72	2	M	26066	0.07
73	1	F	25887	0.07
73	2	N	25887	0.07
74	1	F	25835	0.07
74	2	O	25835	0.07
75	1	F	26263	0.07
75	2	P	26263	0.07
76	1	G	27332	0.05
76	2	H	27332	0.05
77	1	G	25746	0.07
77	2	I	25746	0.07
78	1	G	26224	0.05
78	2	J	26224	0.05
79	1	G	25952	0.07
79	2	K	25952	0.07
80	1	G	26067	0.07
80	2	L	26067	0.07
81	1	G	26137	0.06
81	2	M	26137	0.06
82	1	G	26016	0.07
82	2	N	26016	0.07
83	1	G	26070	0.07
83	2	O	26070	0.07
84	1	G	26459	0.06
84	2	P	26459	0.06
85	1	H	25810	0.06
85	2	I	25810	0.06
86	1	H	26145	0.06
86	2	J	26145	0.06
87	1	H	26022	0.06
87	2	K	26022	0.06
88	1	H	26121	0.07
88	2	L	26121	0.07
89	1	H	26118	0.06
89	2	M	26118	0.06
90	1	H	26064	0.06
90	2	N	26064	0.06
91	1	H	26088	0.07
91	2	O	26088	0.07
92	1	H	26394	0.06
92	2	P	26394	0.06
93	1	I	25789	0.06
93	2	J	25789	0.06
94	1	I	25656	0.06
94	2	K	25656	0.06
95	1	I	25690	0.07
95	2	L	25690	0.07
96	1	I	25920	0.06
96	2	M	25920	0.06
97	1	I	25735	0.07
97	2	N	25735	0.07
98	1	I	25665	0.07
98	2	O	25665	0.07
99	1	I	25771	0.06
99	2	P	25771	0.06
100	1	J	25914	0.06
100	2	K	25914	0.06
101	1	J	26081	0.06
101	2	L	26081	0.06
102	1	J	26193	0.05
102	2	M	26193	0.05
103	1	J	26117	0.05
103	2	N	26117	0.05
104	1	J	26051	0.06
104	2	O	26051	0.06
105	1	J	26153	0.06
105	2	P	26153	0.06
106	1	K	25998	0.06
106	2	L	25998	0.06
107	1	K	25966	0.06
107	2	M	25966	0.06
108	1	K	26045	0.06
108	2	N	26045	0.06
109	1	K	26023	0.06
109	2	O	26023	0.06
110	1	K	26001	0.06
110	2	P	26001	0.06
111	1	L	26316	0.05
111	2	M	26316	0.05
112	1	L	26191	0.06
112	2	N	26191	0.06
113	1	L	26215	0.06
113	2	O	26215	0.06
114	1	L	26223	0.06
114	2	P	26223	0.06
115	1	M	26108	0.06
115	2	N	26108	0.06
116	1	M	26064	0.06
116	2	O	26064	0.06
117	1	M	26191	0.06
117	2	P	26191	0.06
118	1	N	26180	0.06
118	2	O	26180	0.06
119	1	N	26086	0.06
119	2	P	26086	0.06
120	1	O	26086	0.06
120	2	P	26086	0.06

LS refinement shell

Resolution: 2.35→2.41 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.326	548	-
Rwork	0.245	10056	-
obs	-	-	53.53 %