PDB-2vax: Crystal structure of deacetylcephalosporin C acetyltransferase (C...

Basic information

• Entry: Database: PDB / ID: 2vax
• Title: Crystal structure of deacetylcephalosporin C acetyltransferase (Cephalosporin C-soak)
• Components: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
• Keywords: TRANSFERASE / DEACETYLCEPHALOSPORIN C / CEPHALOSPORIN BIOSYNTHESIS / A/B-HYDROLASE FOLD / ANTIBIOTIC BIOSYNTHESIS / ACYLTRANSFERASE / ACETYL TRANSFERASE

Function / homology

Function:

deacetylcephalosporin-C acetyltransferase / deacetylcephalosporin-C acetyltransferase activity / homoserine metabolic process / homoserine O-acetyltransferase activity / methionine biosynthetic process / antibiotic biosynthetic process

Domain/homology:

Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETATE ION / Chem-CSC / Acetyl-CoA--deacetylcephalosporin C acetyltransferase

• Biological species: ACREMONIUM CHRYSOGENUM (fungus)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
• Authors: Lejon, S. / Ellis, J. / Valegard, K.
• Citation: Journal: J.Mol.Biol. / Year: 2008; Title: The Last Step in Cephalosporin C Formation Revealed: Crystal Structures of Deacetylcephalosporin C Acetyltransferase from Acremonium Chrysogenum in Complexes with Reaction Intermediates.; Authors: Lejon, S. / Ellis, J. / Valegard, K.

History

Deposition	Sep 4, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Assembly

Deposited unit

A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• 597 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	596,704	34
Polymers	591,116	12
Non-polymers	5,588	22
Water	3,729	207

1

A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,470	6
Polymers	98,519	2
Non-polymers	951	4
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	4470 Å2
ΔGint	-36.8 kcal/mol
Surface area	31570 Å2
Method	PISA

2

B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,470	6
Polymers	98,519	2
Non-polymers	951	4
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	4880 Å2
ΔGint	-27.1 kcal/mol
Surface area	31350 Å2
Method	PISA

3

D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,411	5
Polymers	98,519	2
Non-polymers	892	3
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	4330 Å2
ΔGint	-20.7 kcal/mol
Surface area	30910 Å2
Method	PISA

4

F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,470	6
Polymers	98,519	2
Non-polymers	951	4
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	3670 Å2
ΔGint	-23.4 kcal/mol
Surface area	30250 Å2
Method	PISA

5

G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,470	6
Polymers	98,519	2
Non-polymers	951	4
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	4260 Å2
ΔGint	-27.2 kcal/mol
Surface area	30410 Å2
Method	PISA

6

C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

hetero molecules

Summary:

• defined by author&software
• 99.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,411	5
Polymers	98,519	2
Non-polymers	892	3
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	4410 Å2
ΔGint	-19.4 kcal/mol
Surface area	31140 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	121.357, 109.288, 195.388
Angle α, β, γ (deg.)	90.00, 90.03, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F
7	2	G
8	2	H
9	2	I
10	2	J
11	2	K
12	2	L
1	3	A
2	3	B
3	3	C
4	3	D
5	3	E
6	3	F
7	3	G
8	3	H
9	3	I
10	3	J
11	3	K
12	3	L
1	4	A
2	4	B
3	4	C
4	4	D
5	4	E
6	4	F
7	4	G
8	4	H
9	4	I
10	4	J
11	4	K
12	4	L
1	5	A
2	5	B
3	5	C
4	5	D
5	5	E
6	5	F
7	5	G
8	5	H
9	5	I
10	5	J
11	5	K
12	5	L
1	6	A
2	6	B
3	6	C
4	6	D
5	6	E
6	6	F
7	6	G
8	6	H
9	6	I
10	6	J
11	6	K
12	6	L
1	7	A
2	7	B
3	7	C
4	7	D
5	7	E
6	7	F
7	7	G
8	7	H
9	7	I
10	7	J
11	7	K
12	7	L
1	8	A
2	8	B
3	8	C
4	8	D
5	8	E
6	8	F
7	8	G
8	8	H
9	8	I
10	8	J
11	8	K
12	8	L
1	9	A
2	9	B
3	9	C
4	9	D
5	9	E
6	9	F
7	9	G
8	9	H
9	9	I
10	9	J
11	9	K
12	9	L
1	10	A
2	10	B
3	10	C
4	10	D
5	10	E
6	10	F
7	10	G
8	10	H
9	10	I
10	10	J
11	10	K
12	10	L
1	11	A
2	11	B
3	11	C
4	11	D
5	11	E
6	11	F
7	11	G
8	11	H
9	11	I
10	11	J
11	11	K
12	11	L
1	12	A
2	12	B
3	12	C
4	12	D
5	12	E
6	12	F
7	12	G
8	12	H
9	12	I
10	12	J
11	12	K
12	12	L

NCS domain segments:

Component-ID: 1 / Refine code: 1

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	ASN	ASN	ARG	ARG	A	A	7 - 33	66 - 92
2	1	ASN	ASN	ARG	ARG	B	B	7 - 33	66 - 92
3	1	ASN	ASN	ARG	ARG	C	C	7 - 33	66 - 92
4	1	ASN	ASN	ARG	ARG	D	D	7 - 33	66 - 92
5	1	ASN	ASN	ARG	ARG	E	E	7 - 33	66 - 92
6	1	ASN	ASN	ARG	ARG	F	F	7 - 33	66 - 92
7	1	ASN	ASN	ARG	ARG	G	G	7 - 33	66 - 92
8	1	ASN	ASN	ARG	ARG	H	H	7 - 33	66 - 92
9	1	ASN	ASN	ARG	ARG	I	I	7 - 33	66 - 92
10	1	ASN	ASN	ARG	ARG	J	J	7 - 33	66 - 92
11	1	ASN	ASN	ARG	ARG	K	K	7 - 33	66 - 92
12	1	ASN	ASN	ARG	ARG	L	L	7 - 33	66 - 92
1	2	VAL	VAL	LEU	LEU	A	A	35 - 59	94 - 118
2	2	VAL	VAL	LEU	LEU	B	B	35 - 59	94 - 118
3	2	VAL	VAL	LEU	LEU	C	C	35 - 59	94 - 118
4	2	VAL	VAL	LEU	LEU	D	D	35 - 59	94 - 118
5	2	VAL	VAL	LEU	LEU	E	E	35 - 59	94 - 118
6	2	VAL	VAL	LEU	LEU	F	F	35 - 59	94 - 118
7	2	VAL	VAL	LEU	LEU	G	G	35 - 59	94 - 118
8	2	VAL	VAL	LEU	LEU	H	H	35 - 59	94 - 118
9	2	VAL	VAL	LEU	LEU	I	I	35 - 59	94 - 118
10	2	VAL	VAL	LEU	LEU	J	J	35 - 59	94 - 118
11	2	VAL	VAL	LEU	LEU	K	K	35 - 59	94 - 118
12	2	VAL	VAL	LEU	LEU	L	L	35 - 59	94 - 118
1	3	SER	SER	VAL	VAL	A	A	61 - 127	120 - 186
2	3	SER	SER	VAL	VAL	B	B	61 - 127	120 - 186
3	3	SER	SER	VAL	VAL	C	C	61 - 127	120 - 186
4	3	SER	SER	VAL	VAL	D	D	61 - 127	120 - 186
5	3	SER	SER	VAL	VAL	E	E	61 - 127	120 - 186
6	3	SER	SER	VAL	VAL	F	F	61 - 127	120 - 186
7	3	SER	SER	VAL	VAL	G	G	61 - 127	120 - 186
8	3	SER	SER	VAL	VAL	H	H	61 - 127	120 - 186
9	3	SER	SER	VAL	VAL	I	I	61 - 127	120 - 186
10	3	SER	SER	VAL	VAL	J	J	61 - 127	120 - 186
11	3	SER	SER	VAL	VAL	K	K	61 - 127	120 - 186
12	3	SER	SER	VAL	VAL	L	L	61 - 127	120 - 186
1	4	ILE	ILE	VAL	VAL	A	A	129 - 139	188 - 198
2	4	ILE	ILE	VAL	VAL	B	B	129 - 139	188 - 198
3	4	ILE	ILE	VAL	VAL	C	C	129 - 139	188 - 198
4	4	ILE	ILE	VAL	VAL	D	D	129 - 139	188 - 198
5	4	ILE	ILE	VAL	VAL	E	E	129 - 139	188 - 198
6	4	ILE	ILE	VAL	VAL	F	F	129 - 139	188 - 198
7	4	ILE	ILE	VAL	VAL	G	G	129 - 139	188 - 198
8	4	ILE	ILE	VAL	VAL	H	H	129 - 139	188 - 198
9	4	ILE	ILE	VAL	VAL	I	I	129 - 139	188 - 198
10	4	ILE	ILE	VAL	VAL	J	J	129 - 139	188 - 198
11	4	ILE	ILE	VAL	VAL	K	K	129 - 139	188 - 198
12	4	ILE	ILE	VAL	VAL	L	L	129 - 139	188 - 198
1	5	GLN	GLN	ALA	ALA	A	A	141 - 159	200 - 218
2	5	GLN	GLN	ALA	ALA	B	B	141 - 159	200 - 218
3	5	GLN	GLN	ALA	ALA	C	C	141 - 159	200 - 218
4	5	GLN	GLN	ALA	ALA	D	D	141 - 159	200 - 218
5	5	GLN	GLN	ALA	ALA	E	E	141 - 159	200 - 218
6	5	GLN	GLN	ALA	ALA	F	F	141 - 159	200 - 218
7	5	GLN	GLN	ALA	ALA	G	G	141 - 159	200 - 218
8	5	GLN	GLN	ALA	ALA	H	H	141 - 159	200 - 218
9	5	GLN	GLN	ALA	ALA	I	I	141 - 159	200 - 218
10	5	GLN	GLN	ALA	ALA	J	J	141 - 159	200 - 218
11	5	GLN	GLN	ALA	ALA	K	K	141 - 159	200 - 218
12	5	GLN	GLN	ALA	ALA	L	L	141 - 159	200 - 218
1	6	PHE	PHE	ALA	ALA	A	A	161 - 217	220 - 276
2	6	PHE	PHE	ALA	ALA	B	B	161 - 217	220 - 276
3	6	PHE	PHE	ALA	ALA	C	C	161 - 217	220 - 276
4	6	PHE	PHE	ALA	ALA	D	D	161 - 217	220 - 276
5	6	PHE	PHE	ALA	ALA	E	E	161 - 217	220 - 276
6	6	PHE	PHE	ALA	ALA	F	F	161 - 217	220 - 276
7	6	PHE	PHE	ALA	ALA	G	G	161 - 217	220 - 276
8	6	PHE	PHE	ALA	ALA	H	H	161 - 217	220 - 276
9	6	PHE	PHE	ALA	ALA	I	I	161 - 217	220 - 276
10	6	PHE	PHE	ALA	ALA	J	J	161 - 217	220 - 276
11	6	PHE	PHE	ALA	ALA	K	K	161 - 217	220 - 276
12	6	PHE	PHE	ALA	ALA	L	L	161 - 217	220 - 276
1	7	LYS	LYS	PHE	PHE	A	A	219 - 235	278 - 294
2	7	LYS	LYS	PHE	PHE	B	B	219 - 235	278 - 294
3	7	LYS	LYS	PHE	PHE	C	C	219 - 235	278 - 294
4	7	LYS	LYS	PHE	PHE	D	D	219 - 235	278 - 294
5	7	LYS	LYS	PHE	PHE	E	E	219 - 235	278 - 294
6	7	LYS	LYS	PHE	PHE	F	F	219 - 235	278 - 294
7	7	LYS	LYS	PHE	PHE	G	G	219 - 235	278 - 294
8	7	LYS	LYS	PHE	PHE	H	H	219 - 235	278 - 294
9	7	LYS	LYS	PHE	PHE	I	I	219 - 235	278 - 294
10	7	LYS	LYS	PHE	PHE	J	J	219 - 235	278 - 294
11	7	LYS	LYS	PHE	PHE	K	K	219 - 235	278 - 294
12	7	LYS	LYS	PHE	PHE	L	L	219 - 235	278 - 294
1	8	MET	MET	ARG	ARG	A	A	237 - 279	296 - 338
2	8	MET	MET	ARG	ARG	B	B	237 - 279	296 - 338
3	8	MET	MET	ARG	ARG	C	C	237 - 279	296 - 338
4	8	MET	MET	ARG	ARG	D	D	237 - 279	296 - 338
5	8	MET	MET	ARG	ARG	E	E	237 - 279	296 - 338
6	8	MET	MET	ARG	ARG	F	F	237 - 279	296 - 338
7	8	MET	MET	ARG	ARG	G	G	237 - 279	296 - 338
8	8	MET	MET	ARG	ARG	H	H	237 - 279	296 - 338
9	8	MET	MET	ARG	ARG	I	I	237 - 279	296 - 338
10	8	MET	MET	ARG	ARG	J	J	237 - 279	296 - 338
11	8	MET	MET	ARG	ARG	K	K	237 - 279	296 - 338
12	8	MET	MET	ARG	ARG	L	L	237 - 279	296 - 338
1	9	ALA	ALA	SER	SER	A	A	282 - 307	341 - 366
2	9	ALA	ALA	SER	SER	B	B	282 - 307	341 - 366
3	9	ALA	ALA	SER	SER	C	C	282 - 307	341 - 366
4	9	ALA	ALA	SER	SER	D	D	282 - 307	341 - 366
5	9	ALA	ALA	SER	SER	E	E	282 - 307	341 - 366
6	9	ALA	ALA	SER	SER	F	F	282 - 307	341 - 366
7	9	ALA	ALA	SER	SER	G	G	282 - 307	341 - 366
8	9	ALA	ALA	SER	SER	H	H	282 - 307	341 - 366
9	9	ALA	ALA	SER	SER	I	I	282 - 307	341 - 366
10	9	ALA	ALA	SER	SER	J	J	282 - 307	341 - 366
11	9	ALA	ALA	SER	SER	K	K	282 - 307	341 - 366
12	9	ALA	ALA	SER	SER	L	L	282 - 307	341 - 366
1	10	GLY	GLY	ALA	ALA	A	A	309 - 330	368 - 389
2	10	GLY	GLY	ALA	ALA	B	B	309 - 330	368 - 389
3	10	GLY	GLY	ALA	ALA	C	C	309 - 330	368 - 389
4	10	GLY	GLY	ALA	ALA	D	D	309 - 330	368 - 389
5	10	GLY	GLY	ALA	ALA	E	E	309 - 330	368 - 389
6	10	GLY	GLY	ALA	ALA	F	F	309 - 330	368 - 389
7	10	GLY	GLY	ALA	ALA	G	G	309 - 330	368 - 389
8	10	GLY	GLY	ALA	ALA	H	H	309 - 330	368 - 389
9	10	GLY	GLY	ALA	ALA	I	I	309 - 330	368 - 389
10	10	GLY	GLY	ALA	ALA	J	J	309 - 330	368 - 389
11	10	GLY	GLY	ALA	ALA	K	K	309 - 330	368 - 389
12	10	GLY	GLY	ALA	ALA	L	L	309 - 330	368 - 389
1	11	SER	SER	GLY	GLY	A	A	332 - 345	391 - 404
2	11	SER	SER	GLY	GLY	B	B	332 - 345	391 - 404
3	11	SER	SER	GLY	GLY	C	C	332 - 345	391 - 404
4	11	SER	SER	GLY	GLY	D	D	332 - 345	391 - 404
5	11	SER	SER	GLY	GLY	E	E	332 - 345	391 - 404
6	11	SER	SER	GLY	GLY	F	F	332 - 345	391 - 404
7	11	SER	SER	GLY	GLY	G	G	332 - 345	391 - 404
8	11	SER	SER	GLY	GLY	H	H	332 - 345	391 - 404
9	11	SER	SER	GLY	GLY	I	I	332 - 345	391 - 404
10	11	SER	SER	GLY	GLY	J	J	332 - 345	391 - 404
11	11	SER	SER	GLY	GLY	K	K	332 - 345	391 - 404
12	11	SER	SER	GLY	GLY	L	L	332 - 345	391 - 404
1	12	SER	SER	ASP	ASP	A	A	347 - 381	406 - 440
2	12	SER	SER	ASP	ASP	B	B	347 - 381	406 - 440
3	12	SER	SER	ASP	ASP	C	C	347 - 381	406 - 440
4	12	SER	SER	ASP	ASP	D	D	347 - 381	406 - 440
5	12	SER	SER	ASP	ASP	E	E	347 - 381	406 - 440
6	12	SER	SER	ASP	ASP	F	F	347 - 381	406 - 440
7	12	SER	SER	ASP	ASP	G	G	347 - 381	406 - 440
8	12	SER	SER	ASP	ASP	H	H	347 - 381	406 - 440
9	12	SER	SER	ASP	ASP	I	I	347 - 381	406 - 440
10	12	SER	SER	ASP	ASP	J	J	347 - 381	406 - 440
11	12	SER	SER	ASP	ASP	K	K	347 - 381	406 - 440
12	12	SER	SER	ASP	ASP	L	L	347 - 381	406 - 440

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9999, -0.0108, 0.01095), (0.01046, -0.9995, 0.03044), (-0.01127, 0.03033, 0.9995)	152.7, 19.97, 0.6275
2	given	(-0.7973, 0.1006, -0.5951), (0.07706, 0.9949, 0.06492), (0.5986, 0.005905, -0.801)	147.6, 0.9931, -18.94
3	given	(0.7981, -0.1, -0.5942), (-0.07633, -0.995, 0.06493), (-0.5977, -0.006466, -0.8017)	57.25, -23.75, 168
4	given	(1, 0.00072, 1.6E-5), (0.00072, -1, 0.000534), (1.6E-5, -0.000534, -1)	60.68, 22.07, 97.7
5	given	(-0.5185, 0.5007, 0.6931), (0.3403, 0.8645, -0.3699), (-0.7844, 0.04406, -0.6187)	110.2, -7.281, 56.21
6	given	(0.528, 0.4876, 0.6953), (0.3848, -0.8672, 0.316), (0.7571, 0.1007, -0.6455)	-8.558, -42.44, 58.06
7	given	(0.5275, -0.4873, -0.6959), (0.3851, 0.8673, -0.3155), (0.7572, -0.1016, 0.6452)	38.16, -54.17, -48.77
8	given	(-0.9999, 0.01186, 0.01086), (0.01152, 0.9995, -0.0304), (-0.01121, -0.03027, -0.9995)	212, 0.06128, 99.62
9	given	(-0.8005, -0.09654, -0.5915), (-0.04778, 0.9941, -0.09757), (0.5975, -0.04984, -0.8004)	157.4, 63.95, 41.78
10	given	(-0.8027, 0.1004, 0.5878), (-0.0501, -0.9936, 0.1013), (0.5942, 0.0519, 0.8026)	156.5, -29.16, -67.97
11	given	(-0.5184, -0.5007, -0.6933), (0.3401, -0.8645, 0.37), (-0.7846, -0.04399, 0.6184)	220.4, -44.9, 44.34

Components

#1: Protein

A B C D E F G H I J K L
ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE / DCPC-ATF / DAC ACETYLTRANSFERASE / DAC-AT / DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE

Details:

Mass: 49259.664 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACREMONIUM CHRYSOGENUM (fungus) / Plasmid: PTWIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39058, deacetylcephalosporin-C acetyltransferase

#2: Chemical

A-1383 B-1384 C-1383 D-1383 E-1383 F-1384 G-1383 H-1383 I-1384 J-1385 K-1385 L-1383
ChemComp-CSC / 4-(3-ACETOXYMETHYL-2-CARBOXY-8-OXO-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-EN-7-YLCARBAMOYL)-1-CARBOXY-BUTYL-AMMONIUM / CEPHALOSPORIN C

Details:

Mass: 416.426 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₆H₂₂N₃O₈S / Comment: antibiotic*YM

#3: Chemical

A-1384 B-1385 C-1384 D-1384 E-1384 F-1385 G-1384 H-1384 I-1385 L-1384
ChemComp-ACT / ACETATE ION

Details:

Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₃O₂

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.52 ų/Da / Density % sol: 51 % / Description: NONE
• Crystal grow: Details: 18-19% PEG 4000, 0.1M IMIDAZOLE, 0.5M NACL, 0.2M SODIUM ACETATE

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
• Detector: Type: ADSC CCD / Detector: CCD / Date: Mar 9, 2007 / Details: TOROIDAL MIRROR
• Radiation: Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.931 Å / Relative weight: 1
• Reflection: Resolution: 2.6→65.09 Å / Num. obs: 156738 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.8 % / R_merge(I) obs: 0.07 / Net I/σ(I): 14.7
• Reflection shell: Resolution: 2.6→2.74 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.22 / Mean I/σ(I) obs: 5.8 / % possible all: 99.7

Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
REFMAC		phasing

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→62.75 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.901 / SU B: 10.879 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.715 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 241-267 ARE DISORDERED.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24	3414	2.2 %	RANDOM
Rwork	0.211	-	-	-
obs	0.212	153301	99.8 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 28.99 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.33 Å2	0 Å2	-0.07 Å2
2-	-	2.1 Å2	0 Å2
3-	-	-	-1.77 Å2

Refinement step

Cycle: LAST / Resolution: 2.6→62.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32625	0	340	207	33172

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	33955
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.909	1.952	46024
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.994	5	4145
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.354	22.61	1640
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.107	15	5358
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.932	15	336
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	4911
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	26528
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	15295
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	23563
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	1125
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	0.291	0.2	253
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.233	0.2	19
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	0.868	1.5	21088
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.414	2	33285
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.169	3	14489
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.642	4.5	12694
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	197	tight positional	0.06	0.05
1	2	B	197	tight positional	0.11	0.05
1	3	C	197	tight positional	0.07	0.05
1	4	D	197	tight positional	0.07	0.05
1	5	E	197	tight positional	0.07	0.05
1	6	F	197	tight positional	0.06	0.05
1	7	G	197	tight positional	0.13	0.05
1	8	H	197	tight positional	0.1	0.05
1	9	I	197	tight positional	0.07	0.05
1	10	J	197	tight positional	0.08	0.05
1	11	K	197	tight positional	0.07	0.05
1	12	L	197	tight positional	0.06	0.05
2	1	A	189	tight positional	0.06	0.05
2	2	B	189	tight positional	0.06	0.05
2	3	C	189	tight positional	0.06	0.05
2	4	D	189	tight positional	0.06	0.05
2	5	E	189	tight positional	0.05	0.05
2	6	F	189	tight positional	0.07	0.05
2	7	G	189	tight positional	0.07	0.05
2	8	H	189	tight positional	0.06	0.05
2	9	I	189	tight positional	0.06	0.05
2	10	J	189	tight positional	0.05	0.05
2	11	K	189	tight positional	0.05	0.05
2	12	L	189	tight positional	0.06	0.05
3	1	A	469	tight positional	0.05	0.05
3	2	B	469	tight positional	0.05	0.05
3	3	C	469	tight positional	0.07	0.05
3	4	D	469	tight positional	0.07	0.05
3	5	E	469	tight positional	0.05	0.05
3	6	F	469	tight positional	0.06	0.05
3	7	G	469	tight positional	0.06	0.05
3	8	H	469	tight positional	0.06	0.05
3	9	I	469	tight positional	0.05	0.05
3	10	J	469	tight positional	0.06	0.05
3	11	K	469	tight positional	0.06	0.05
3	12	L	469	tight positional	0.06	0.05
4	1	A	83	tight positional	0.06	0.05
4	2	B	83	tight positional	0.06	0.05
4	3	C	83	tight positional	0.06	0.05
4	4	D	83	tight positional	0.07	0.05
4	5	E	83	tight positional	0.06	0.05
4	6	F	83	tight positional	0.07	0.05
4	7	G	83	tight positional	0.08	0.05
4	8	H	83	tight positional	0.05	0.05
4	9	I	83	tight positional	0.05	0.05
4	10	J	83	tight positional	0.08	0.05
4	11	K	83	tight positional	0.07	0.05
4	12	L	83	tight positional	0.06	0.05
5	1	A	136	tight positional	0.08	0.05
5	2	B	136	tight positional	0.05	0.05
5	3	C	136	tight positional	0.06	0.05
5	4	D	136	tight positional	0.06	0.05
5	5	E	136	tight positional	0.06	0.05
5	6	F	136	tight positional	0.05	0.05
5	7	G	136	tight positional	0.06	0.05
5	8	H	136	tight positional	0.06	0.05
5	9	I	136	tight positional	0.05	0.05
5	10	J	136	tight positional	0.06	0.05
5	11	K	136	tight positional	0.06	0.05
5	12	L	136	tight positional	0.05	0.05
6	1	A	457	tight positional	0.08	0.05
6	2	B	457	tight positional	0.05	0.05
6	3	C	457	tight positional	0.06	0.05
6	4	D	457	tight positional	0.06	0.05
6	5	E	457	tight positional	0.05	0.05
6	6	F	457	tight positional	0.08	0.05
6	7	G	457	tight positional	0.06	0.05
6	8	H	457	tight positional	0.06	0.05
6	9	I	457	tight positional	0.06	0.05
6	10	J	457	tight positional	0.05	0.05
6	11	K	457	tight positional	0.06	0.05
6	12	L	457	tight positional	0.05	0.05
7	1	A	140	tight positional	0.07	0.05
7	2	B	140	tight positional	0.05	0.05
7	3	C	140	tight positional	0.05	0.05
7	4	D	140	tight positional	0.05	0.05
7	5	E	140	tight positional	0.07	0.05
7	6	F	140	tight positional	0.06	0.05
7	7	G	140	tight positional	0.06	0.05
7	8	H	140	tight positional	0.06	0.05
7	9	I	140	tight positional	0.05	0.05
7	10	J	140	tight positional	0.06	0.05
7	11	K	140	tight positional	0.06	0.05
7	12	L	140	tight positional	0.06	0.05
8	1	A	96	tight positional	0.05	0.05
8	2	B	96	tight positional	0.05	0.05
8	3	C	96	tight positional	0.04	0.05
8	4	D	96	tight positional	0.05	0.05
8	5	E	96	tight positional	0.05	0.05
8	6	F	96	tight positional	0.06	0.05
8	7	G	96	tight positional	0.05	0.05
8	8	H	96	tight positional	0.06	0.05
8	9	I	96	tight positional	0.05	0.05
8	10	J	96	tight positional	0.06	0.05
8	11	K	96	tight positional	0.06	0.05
8	12	L	96	tight positional	0.05	0.05
9	1	A	203	tight positional	0.05	0.05
9	2	B	203	tight positional	0.05	0.05
9	3	C	203	tight positional	0.06	0.05
9	4	D	203	tight positional	0.06	0.05
9	5	E	203	tight positional	0.05	0.05
9	6	F	203	tight positional	0.05	0.05
9	7	G	203	tight positional	0.06	0.05
9	8	H	203	tight positional	0.06	0.05
9	9	I	203	tight positional	0.05	0.05
9	10	J	203	tight positional	0.06	0.05
9	11	K	203	tight positional	0.06	0.05
9	12	L	203	tight positional	0.05	0.05
10	1	A	151	tight positional	0.08	0.05
10	2	B	151	tight positional	0.06	0.05
10	3	C	151	tight positional	0.05	0.05
10	4	D	151	tight positional	0.11	0.05
10	5	E	151	tight positional	0.06	0.05
10	6	F	151	tight positional	0.05	0.05
10	7	G	151	tight positional	0.06	0.05
10	8	H	151	tight positional	0.06	0.05
10	9	I	151	tight positional	0.06	0.05
10	10	J	151	tight positional	0.05	0.05
10	11	K	151	tight positional	0.05	0.05
10	12	L	151	tight positional	0.05	0.05
11	1	A	110	tight positional	0.06	0.05
11	2	B	110	tight positional	0.05	0.05
11	3	C	110	tight positional	0.06	0.05
11	4	D	110	tight positional	0.06	0.05
11	5	E	110	tight positional	0.06	0.05
11	6	F	110	tight positional	0.05	0.05
11	7	G	110	tight positional	0.04	0.05
11	8	H	110	tight positional	0.04	0.05
11	9	I	110	tight positional	0.05	0.05
11	10	J	110	tight positional	0.05	0.05
11	11	K	110	tight positional	0.05	0.05
11	12	L	110	tight positional	0.05	0.05
12	1	A	273	tight positional	0.08	0.05
12	2	B	273	tight positional	0.13	0.05
12	3	C	273	tight positional	0.08	0.05
12	4	D	273	tight positional	0.08	0.05
12	5	E	273	tight positional	0.08	0.05
12	6	F	273	tight positional	0.13	0.05
12	7	G	273	tight positional	0.08	0.05
12	8	H	273	tight positional	0.13	0.05
12	9	I	273	tight positional	0.13	0.05
12	10	J	273	tight positional	0.08	0.05
12	11	K	273	tight positional	0.08	0.05
12	12	L	273	tight positional	0.08	0.05
1	1	A	197	tight thermal	0.15	0.5
1	2	B	197	tight thermal	0.19	0.5
1	3	C	197	tight thermal	0.22	0.5
1	4	D	197	tight thermal	0.21	0.5
1	5	E	197	tight thermal	0.15	0.5
1	6	F	197	tight thermal	0.16	0.5
1	7	G	197	tight thermal	0.13	0.5
1	8	H	197	tight thermal	0.13	0.5
1	9	I	197	tight thermal	0.19	0.5
1	10	J	197	tight thermal	0.32	0.5
1	11	K	197	tight thermal	0.33	0.5
1	12	L	197	tight thermal	0.16	0.5
2	1	A	189	tight thermal	0.19	0.5
2	2	B	189	tight thermal	0.13	0.5
2	3	C	189	tight thermal	0.24	0.5
2	4	D	189	tight thermal	0.23	0.5
2	5	E	189	tight thermal	0.18	0.5
2	6	F	189	tight thermal	0.18	0.5
2	7	G	189	tight thermal	0.2	0.5
2	8	H	189	tight thermal	0.2	0.5
2	9	I	189	tight thermal	0.12	0.5
2	10	J	189	tight thermal	0.29	0.5
2	11	K	189	tight thermal	0.31	0.5
2	12	L	189	tight thermal	0.18	0.5
3	1	A	469	tight thermal	0.15	0.5
3	2	B	469	tight thermal	0.15	0.5
3	3	C	469	tight thermal	0.23	0.5
3	4	D	469	tight thermal	0.23	0.5
3	5	E	469	tight thermal	0.15	0.5
3	6	F	469	tight thermal	0.15	0.5
3	7	G	469	tight thermal	0.16	0.5
3	8	H	469	tight thermal	0.16	0.5
3	9	I	469	tight thermal	0.15	0.5
3	10	J	469	tight thermal	0.29	0.5
3	11	K	469	tight thermal	0.3	0.5
3	12	L	469	tight thermal	0.15	0.5
4	1	A	83	tight thermal	0.14	0.5
4	2	B	83	tight thermal	0.2	0.5
4	3	C	83	tight thermal	0.24	0.5
4	4	D	83	tight thermal	0.25	0.5
4	5	E	83	tight thermal	0.15	0.5
4	6	F	83	tight thermal	0.17	0.5
4	7	G	83	tight thermal	0.15	0.5
4	8	H	83	tight thermal	0.16	0.5
4	9	I	83	tight thermal	0.18	0.5
4	10	J	83	tight thermal	0.35	0.5
4	11	K	83	tight thermal	0.33	0.5
4	12	L	83	tight thermal	0.18	0.5
5	1	A	136	tight thermal	0.16	0.5
5	2	B	136	tight thermal	0.16	0.5
5	3	C	136	tight thermal	0.18	0.5
5	4	D	136	tight thermal	0.19	0.5
5	5	E	136	tight thermal	0.16	0.5
5	6	F	136	tight thermal	0.17	0.5
5	7	G	136	tight thermal	0.2	0.5
5	8	H	136	tight thermal	0.2	0.5
5	9	I	136	tight thermal	0.17	0.5
5	10	J	136	tight thermal	0.32	0.5
5	11	K	136	tight thermal	0.31	0.5
5	12	L	136	tight thermal	0.14	0.5
6	1	A	457	tight thermal	0.14	0.5
6	2	B	457	tight thermal	0.13	0.5
6	3	C	457	tight thermal	0.13	0.5
6	4	D	457	tight thermal	0.13	0.5
6	5	E	457	tight thermal	0.14	0.5
6	6	F	457	tight thermal	0.15	0.5
6	7	G	457	tight thermal	0.17	0.5
6	8	H	457	tight thermal	0.17	0.5
6	9	I	457	tight thermal	0.14	0.5
6	10	J	457	tight thermal	0.2	0.5
6	11	K	457	tight thermal	0.2	0.5
6	12	L	457	tight thermal	0.15	0.5
7	1	A	140	tight thermal	0.15	0.5
7	2	B	140	tight thermal	0.16	0.5
7	3	C	140	tight thermal	0.15	0.5
7	4	D	140	tight thermal	0.16	0.5
7	5	E	140	tight thermal	0.15	0.5
7	6	F	140	tight thermal	0.19	0.5
7	7	G	140	tight thermal	0.13	0.5
7	8	H	140	tight thermal	0.12	0.5
7	9	I	140	tight thermal	0.16	0.5
7	10	J	140	tight thermal	0.13	0.5
7	11	K	140	tight thermal	0.13	0.5
7	12	L	140	tight thermal	0.19	0.5
8	1	A	96	tight thermal	0.09	0.5
8	2	B	96	tight thermal	0.14	0.5
8	3	C	96	tight thermal	0.13	0.5
8	4	D	96	tight thermal	0.13	0.5
8	5	E	96	tight thermal	0.09	0.5
8	6	F	96	tight thermal	0.11	0.5
8	7	G	96	tight thermal	0.12	0.5
8	8	H	96	tight thermal	0.12	0.5
8	9	I	96	tight thermal	0.13	0.5
8	10	J	96	tight thermal	0.19	0.5
8	11	K	96	tight thermal	0.19	0.5
8	12	L	96	tight thermal	0.11	0.5
9	1	A	203	tight thermal	0.11	0.5
9	2	B	203	tight thermal	0.16	0.5
9	3	C	203	tight thermal	0.18	0.5
9	4	D	203	tight thermal	0.17	0.5
9	5	E	203	tight thermal	0.11	0.5
9	6	F	203	tight thermal	0.16	0.5
9	7	G	203	tight thermal	0.13	0.5
9	8	H	203	tight thermal	0.13	0.5
9	9	I	203	tight thermal	0.16	0.5
9	10	J	203	tight thermal	0.27	0.5
9	11	K	203	tight thermal	0.28	0.5
9	12	L	203	tight thermal	0.15	0.5
10	1	A	151	tight thermal	0.15	0.5
10	2	B	151	tight thermal	0.15	0.5
10	3	C	151	tight thermal	0.13	0.5
10	4	D	151	tight thermal	0.12	0.5
10	5	E	151	tight thermal	0.15	0.5
10	6	F	151	tight thermal	0.12	0.5
10	7	G	151	tight thermal	0.15	0.5
10	8	H	151	tight thermal	0.16	0.5
10	9	I	151	tight thermal	0.16	0.5
10	10	J	151	tight thermal	0.21	0.5
10	11	K	151	tight thermal	0.22	0.5
10	12	L	151	tight thermal	0.12	0.5
11	1	A	110	tight thermal	0.16	0.5
11	2	B	110	tight thermal	0.13	0.5
11	3	C	110	tight thermal	0.13	0.5
11	4	D	110	tight thermal	0.13	0.5
11	5	E	110	tight thermal	0.15	0.5
11	6	F	110	tight thermal	0.14	0.5
11	7	G	110	tight thermal	0.15	0.5
11	8	H	110	tight thermal	0.13	0.5
11	9	I	110	tight thermal	0.11	0.5
11	10	J	110	tight thermal	0.12	0.5
11	11	K	110	tight thermal	0.13	0.5
11	12	L	110	tight thermal	0.14	0.5
12	1	A	273	tight thermal	0.15	0.5
12	2	B	273	tight thermal	0.13	0.5
12	3	C	273	tight thermal	0.12	0.5
12	4	D	273	tight thermal	0.12	0.5
12	5	E	273	tight thermal	0.15	0.5
12	6	F	273	tight thermal	0.15	0.5
12	7	G	273	tight thermal	0.14	0.5
12	8	H	273	tight thermal	0.14	0.5
12	9	I	273	tight thermal	0.14	0.5
12	10	J	273	tight thermal	0.16	0.5
12	11	K	273	tight thermal	0.16	0.5
12	12	L	273	tight thermal	0.15	0.5

LS refinement shell

Resolution: 2.6→2.67 Å / Total num. of bins used: 20 /

	Rfactor	Num. reflection
Rfree	0	0
Rwork	0.239	11466