PDB-2g0b: The structure of FeeM, an N-acyl amino acid synthase from uncultu...

Basic information

• Entry: Database: PDB / ID: 2g0b
• Title: The structure of FeeM, an N-acyl amino acid synthase from uncultured soil microbes
• Components: FeeM
• Keywords: TRANSFERASE / N-acyl transferase / environmental DNA / protein-product complex / antibiotic synthase
• Function / homology: Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / identical protein binding / Alpha Beta / N-DODECANOYL-L-TYROSINE / Long-chain N-acyl amino acid synthase
• Biological species: uncultured bacterium (environmental samples)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
• Authors: Van Wagoner, R.M. / Clardy, J.
• Citation: Journal: Structure / Year: 2006; Title: FeeM, an N-Acyl Amino Acid Synthase from an Uncultured Soil Microbe: Structure, Mechanism, and Acyl Carrier Protein Binding.; Authors: Van Wagoner, R.M. / Clardy, J.

History

Deposition	Feb 11, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: FeeM

B: FeeM

C: FeeM

D: FeeM

E: FeeM

F: FeeM

G: FeeM

H: FeeM

hetero molecules

Summary:

• 177 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	177,154	16
Polymers	174,246	8
Non-polymers	2,908	8
Water	162	9

1

A: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	18	1

Symmetry operations:

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

2

B: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

3

C: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

4

D: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

5

E: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

6

F: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

7

G: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

8

H: FeeM

hetero molecules

Summary:

• defined by author
• 22.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	22,144	2
Polymers	21,781	1
Non-polymers	363	1
Water	0

Symmetry operations:

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

9

A: FeeM

B: FeeM

hetero molecules

A: FeeM

B: FeeM

hetero molecules

Summary:

• defined by software
• 88.6 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	88,577	8
Polymers	87,123	4
Non-polymers	1,454	4
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	8_665	-y+1,-x+1,-z	1

Calculated values:

Buried area	13490 Å2
ΔGint	-63 kcal/mol
Surface area	29950 Å2
Method	PISA

10

A: FeeM

B: FeeM

hetero molecules

Summary:

• defined by software
• 44.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,288	4
Polymers	43,561	2
Non-polymers	727	2
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PQS

11

C: FeeM

D: FeeM

hetero molecules

Summary:

• defined by software
• 44.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,288	4
Polymers	43,561	2
Non-polymers	727	2
Water	0

Symmetry operations:

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

Calculated values:

Method	PQS

12

E: FeeM

F: FeeM

hetero molecules

Summary:

• defined by software
• 44.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,288	4
Polymers	43,561	2
Non-polymers	727	2
Water	0

Symmetry operations:

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

Calculated values:

Method	PQS

13

G: FeeM

H: FeeM

hetero molecules

Summary:

• defined by software
• 44.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,288	4
Polymers	43,561	2
Non-polymers	727	2
Water	0

Symmetry operations:

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

Calculated values:

Method	PQS

Unit cell

Length a, b, c (Å)	182.832, 182.832, 287.429
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4122

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	A
10	1	B
11	1	C
12	1	D
13	1	E
14	1	F
15	1	G
16	1	H
17	1	A
18	1	B
19	1	C
20	1	D
21	1	E
22	1	F
23	1	G
24	1	H
1	2	A
2	2	D
3	2	E
4	2	H
5	2	A
6	2	D
7	2	E
8	2	H
9	2	A
10	2	D
11	2	E
12	2	H
13	2	A
14	2	D
15	2	E
16	2	H
1	3	B
2	3	C
3	3	F
4	3	G
5	3	B
6	3	C
7	3	F
8	3	G
9	3	B
10	3	C
11	3	F
12	3	G
13	3	B
14	3	C
15	3	F
16	3	G

NCS domain segments:

Refine code: 4

Dom-ID	Component-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	1	GLU	GLU	LEU	LEU	A	A	15 - 52	17 - 54
2	1	1	GLU	GLU	LEU	LEU	B	B	15 - 52	17 - 54
3	1	1	GLU	GLU	LEU	LEU	C	C	15 - 52	17 - 54
4	1	1	GLU	GLU	LEU	LEU	D	D	15 - 52	17 - 54
5	1	1	GLU	GLU	LEU	LEU	E	E	15 - 52	17 - 54
6	1	1	GLU	GLU	LEU	LEU	F	F	15 - 52	17 - 54
7	1	1	GLU	GLU	LEU	LEU	G	G	15 - 52	17 - 54
8	1	1	GLU	GLU	LEU	LEU	H	H	15 - 52	17 - 54
9	2	1	LEU	LEU	MET	MET	A	A	58 - 100	60 - 102
10	2	1	LEU	LEU	MET	MET	B	B	58 - 100	60 - 102
11	2	1	LEU	LEU	MET	MET	C	C	58 - 100	60 - 102
12	2	1	LEU	LEU	MET	MET	D	D	58 - 100	60 - 102
13	2	1	LEU	LEU	MET	MET	E	E	58 - 100	60 - 102
14	2	1	LEU	LEU	MET	MET	F	F	58 - 100	60 - 102
15	2	1	LEU	LEU	MET	MET	G	G	58 - 100	60 - 102
16	2	1	LEU	LEU	MET	MET	H	H	58 - 100	60 - 102
17	3	1	ALA	ALA	THR	THR	A	A	119 - 184	121 - 186
18	3	1	ALA	ALA	THR	THR	B	B	119 - 184	121 - 186
19	3	1	ALA	ALA	THR	THR	C	C	119 - 184	121 - 186
20	3	1	ALA	ALA	THR	THR	D	D	119 - 184	121 - 186
21	3	1	ALA	ALA	THR	THR	E	E	119 - 184	121 - 186
22	3	1	ALA	ALA	THR	THR	F	F	119 - 184	121 - 186
23	3	1	ALA	ALA	THR	THR	G	G	119 - 184	121 - 186
24	3	1	ALA	ALA	THR	THR	H	H	119 - 184	121 - 186
1	1	2	GLY	GLY	ASN	ASN	A	A	-1 - 14	1 - 16
2	1	2	THR	THR	ASN	ASN	D	D	2 - 14	4 - 16
3	1	2	THR	THR	ASN	ASN	E	E	2 - 14	4 - 16
4	1	2	ARG	ARG	ASN	ASN	H	H	4 - 14	6 - 16
5	2	2	PHE	PHE	VAL	VAL	A	A	53 - 57	55 - 59
6	2	2	PHE	PHE	VAL	VAL	D	D	53 - 57	55 - 59
7	2	2	PHE	PHE	VAL	VAL	E	E	53 - 57	55 - 59
8	2	2	PHE	PHE	VAL	VAL	H	H	53 - 57	55 - 59
9	3	2	ASP	ASP	ALA	ALA	A	A	101 - 118	103 - 120
10	3	2	ASP	ASP	ALA	ALA	D	D	101 - 118	103 - 120
11	3	2	ASP	ASP	ALA	ALA	E	E	101 - 118	103 - 120
12	3	2	ASP	ASP	ALA	ALA	H	H	101 - 118	103 - 120
13	4	2	LEU	LEU	MET	MET	A	A	185 - 190	187 - 192
14	4	2	LEU	LEU	ASP	ASP	D	D	185 - 191	187 - 193
15	4	2	LEU	LEU	ASP	ASP	E	E	185 - 191	187 - 193
16	4	2	LEU	LEU	MET	MET	H	H	185 - 190	187 - 192
1	1	3	THR	THR	ASN	ASN	B	B	2 - 14	4 - 16
2	1	3	THR	THR	ASN	ASN	C	C	2 - 14	4 - 16
3	1	3	THR	THR	ASN	ASN	F	F	2 - 14	4 - 16
4	1	3	LYS	LYS	ASN	ASN	G	G	5 - 14	7 - 16
5	2	3	PHE	PHE	VAL	VAL	B	B	53 - 57	55 - 59
6	2	3	PHE	PHE	VAL	VAL	C	C	53 - 57	55 - 59
7	2	3	PHE	PHE	VAL	VAL	F	F	53 - 57	55 - 59
8	2	3	PHE	PHE	VAL	VAL	G	G	53 - 57	55 - 59
9	3	3	ASP	ASP	ALA	ALA	B	B	101 - 118	103 - 120
10	3	3	ASP	ASP	ALA	ALA	C	C	101 - 118	103 - 120
11	3	3	ASP	ASP	ALA	ALA	F	F	101 - 118	103 - 120
12	3	3	ASP	ASP	ALA	ALA	G	G	101 - 118	103 - 120
13	4	3	LEU	LEU	MET	MET	B	B	185 - 190	187 - 192
14	4	3	LEU	LEU	LEU	LEU	C	C	185	187
15	4	3	LEU	LEU	LEU	LEU	F	F	185	187
16	4	3	LEU	LEU	LEU	LEU	G	G	185	187

NCS ensembles :

ID
1
2
3

• Details: The biological unit appears to be a monomer at physiological concentrations. There are 8 biological units in the asymmetric unit arranged as 4 dimers (chains A & B, chains C & D, chains E & F, and chains G & H

Components

#1: Protein

A B C D E F G H
FeeM

Details:

Mass: 21780.721 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: feem / Plasmid: pET42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8KNZ7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

#2: Chemical

A-400 B-401 C-402 D-403 E-404 F-405 G-406 H-407
ChemComp-NLT / N-DODECANOYL-L-TYROSINE / (S)-N-(DODECANOYL)-2-AMINO-3-(4-HYDROXYPHENYL)-PROPANOIC ACID / N-LAURYL-L-TYROSINE / N-LAUROYL-L-TYROSINE

Details:

Mass: 363.491 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₃₃NO₄

#3: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.6 ų/Da / Density % sol: 65.6 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10 ; Details: 4.06 M NaCl, 50 mM glycine, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9795, 0.9422, 0.9793
• Detector: Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2003
• Radiation: Monochromator: Si [1 1 1] / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.9422	1
3	0.9793	1

• Reflection: Redundancy: 16.4 % / Number: 801973 / R_merge(I) obs: 0.081 / D res high: 2.99 Å / D res low: 129.1 Å
• Reflection: Resolution: 3→129.1 Å / Num. all: 48895 / Num. obs: 48895 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.4 % / R_merge(I) obs: 0.081 / Net I/σ(I): 7.8737
• Reflection shell: Resolution: 3→3.15 Å / Redundancy: 16.9 % / R_merge(I) obs: 0.16 / Mean I/σ(I) obs: 1.31 / Num. measured all: 110846 / Num. unique all: 6574 / % possible all: 100

Phasing

• Phasing: Method: MAD

Phasing set

ID
1
2
3

• Phasing MAD: D res high: 3.5 Å / D res low: 19.99 Å / FOM acentric: 0.513 / FOM centric: 0.365 / Reflection acentric: 27346 / Reflection centric: 3019

Phasing MAD set

Highest resolution: 3.5 Å / Lowest resolution: 19.99 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	27341	3006
ISO_2	0.758	0.706	1.084	0.957	27333	2950
ISO_3	0.839	0.803	0.698	0.593	27336	2989
ANO_1	0.769	0	1.152	0	27337	0
ANO_2	0.717	0	1.465	0	27307	0
ANO_3	0.789	0	1.071	0	27329	0

Phasing MAD set

Resolution (Å)	Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime	F prime
3.5-20	1	1	1	0.9795	7.09801	-2.19
3.5-20	1	1	2	0.9422	10.21519	-18.1549
3.5-20	1	1	3	0.9793	5.20917	-12.33175

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	12.44-19.99	0	0	0	0	404	138
ISO_1	9.8-12.44	0	0	0	0	601	149
ISO_1	8.34-9.8	0	0	0	0	741	152
ISO_1	7.39-8.34	0	0	0	0	867	134
ISO_1	6.7-7.39	0	0	0	0	969	144
ISO_1	6.17-6.7	0	0	0	0	1079	141
ISO_1	5.75-6.17	0	0	0	0	1163	150
ISO_1	5.41-5.75	0	0	0	0	1264	154
ISO_1	5.12-5.41	0	0	0	0	1329	155
ISO_1	4.88-5.12	0	0	0	0	1416	141
ISO_1	4.66-4.88	0	0	0	0	1474	150
ISO_1	4.47-4.66	0	0	0	0	1523	145
ISO_1	4.31-4.47	0	0	0	0	1594	146
ISO_1	4.16-4.31	0	0	0	0	1691	150
ISO_1	4.02-4.16	0	0	0	0	1730	168
ISO_1	3.9-4.02	0	0	0	0	1782	153
ISO_1	3.79-3.9	0	0	0	0	1831	160
ISO_1	3.68-3.79	0	0	0	0	1912	162
ISO_1	3.59-3.68	0	0	0	0	1934	151
ISO_1	3.5-3.59	0	0	0	0	2037	163
ANO_1	12.44-19.99	0.268	0	4.845	0	402	0
ANO_1	9.8-12.44	0.29	0	4.569	0	600	0
ANO_1	8.34-9.8	0.303	0	4.423	0	741	0
ANO_1	7.39-8.34	0.362	0	3.6	0	867	0
ANO_1	6.7-7.39	0.439	0	2.855	0	969	0
ANO_1	6.17-6.7	0.493	0	2.526	0	1079	0
ANO_1	5.75-6.17	0.593	0	1.934	0	1162	0
ANO_1	5.41-5.75	0.678	0	1.512	0	1264	0
ANO_1	5.12-5.41	0.702	0	1.432	0	1329	0
ANO_1	4.88-5.12	0.731	0	1.19	0	1416	0
ANO_1	4.66-4.88	0.762	0	1.112	0	1474	0
ANO_1	4.47-4.66	0.795	0	0.962	0	1523	0
ANO_1	4.31-4.47	0.862	0	0.782	0	1594	0
ANO_1	4.16-4.31	0.884	0	0.694	0	1691	0
ANO_1	4.02-4.16	0.914	0	0.571	0	1730	0
ANO_1	3.9-4.02	0.944	0	0.491	0	1782	0
ANO_1	3.79-3.9	0.965	0	0.398	0	1831	0
ANO_1	3.68-3.79	0.983	0	0.36	0	1912	0
ANO_1	3.59-3.68	0.988	0	0.288	0	1934	0
ANO_1	3.5-3.59	0.99	0	0.254	0	2037	0
ISO_2	12.44-19.99	0.494	0.513	2.213	1.691	401	125
ISO_2	9.8-12.44	0.472	0.486	2.364	1.657	598	144
ISO_2	8.34-9.8	0.483	0.492	2.254	1.744	740	150
ISO_2	7.39-8.34	0.577	0.546	1.904	1.411	867	131
ISO_2	6.7-7.39	0.587	0.536	1.755	1.368	969	141
ISO_2	6.17-6.7	0.588	0.624	1.723	1.165	1079	140
ISO_2	5.75-6.17	0.609	0.656	1.529	1.088	1163	145
ISO_2	5.41-5.75	0.692	0.742	1.256	0.86	1264	152
ISO_2	5.12-5.41	0.751	0.784	1.156	0.882	1329	154
ISO_2	4.88-5.12	0.805	0.789	1.004	0.797	1416	139
ISO_2	4.66-4.88	0.851	0.884	0.854	0.572	1474	150
ISO_2	4.47-4.66	0.898	0.919	0.752	0.472	1523	143
ISO_2	4.31-4.47	0.922	0.908	0.656	0.503	1594	143
ISO_2	4.16-4.31	0.906	0.916	0.615	0.374	1691	146
ISO_2	4.02-4.16	0.92	0.912	0.573	0.436	1729	165
ISO_2	3.9-4.02	0.919	0.909	0.513	0.414	1782	152
ISO_2	3.79-3.9	0.914	0.936	0.432	0.351	1831	159
ISO_2	3.68-3.79	0.935	0.954	0.424	0.268	1912	159
ISO_2	3.59-3.68	0.969	0.981	0.244	0.216	1934	151
ISO_2	3.5-3.59	0.92	0.939	0.346	0.228	2037	161
ANO_2	12.44-19.99	0.245	0	5.791	0	391	0
ANO_2	9.8-12.44	0.256	0	5.51	0	592	0
ANO_2	8.34-9.8	0.287	0	5.066	0	739	0
ANO_2	7.39-8.34	0.331	0	4.316	0	867	0
ANO_2	6.7-7.39	0.394	0	3.399	0	968	0
ANO_2	6.17-6.7	0.453	0	2.989	0	1079	0
ANO_2	5.75-6.17	0.533	0	2.49	0	1163	0
ANO_2	5.41-5.75	0.626	0	1.957	0	1263	0
ANO_2	5.12-5.41	0.668	0	1.666	0	1329	0
ANO_2	4.88-5.12	0.691	0	1.523	0	1415	0
ANO_2	4.66-4.88	0.716	0	1.383	0	1474	0
ANO_2	4.47-4.66	0.787	0	1.147	0	1523	0
ANO_2	4.31-4.47	0.849	0	0.95	0	1593	0
ANO_2	4.16-4.31	0.862	0	0.865	0	1691	0
ANO_2	4.02-4.16	0.915	0	0.713	0	1728	0
ANO_2	3.9-4.02	0.949	0	0.591	0	1783	0
ANO_2	3.79-3.9	0.959	0	0.475	0	1831	0
ANO_2	3.68-3.79	0.976	0	0.431	0	1911	0
ANO_2	3.59-3.68	0.986	0	0.35	0	1934	0
ANO_2	3.5-3.59	0.991	0	0.31	0	2033	0
ISO_3	12.44-19.99	0.704	0.695	1.054	0.904	401	136
ISO_3	9.8-12.44	0.647	0.661	1.168	0.905	601	149
ISO_3	8.34-9.8	0.668	0.663	1.27	0.859	741	149
ISO_3	7.39-8.34	0.753	0.74	1.003	0.712	867	134
ISO_3	6.7-7.39	0.768	0.733	1.027	0.812	969	143
ISO_3	6.17-6.7	0.803	0.804	0.971	0.632	1079	140
ISO_3	5.75-6.17	0.834	0.825	0.899	0.59	1163	148
ISO_3	5.41-5.75	0.873	0.923	0.806	0.553	1264	153
ISO_3	5.12-5.41	0.865	0.831	0.728	0.587	1329	155
ISO_3	4.88-5.12	0.904	0.871	0.671	0.508	1416	141
ISO_3	4.66-4.88	0.905	0.952	0.599	0.403	1474	150
ISO_3	4.47-4.66	0.927	0.926	0.525	0.341	1523	145
ISO_3	4.31-4.47	0.93	0.872	0.452	0.332	1594	144
ISO_3	4.16-4.31	0.94	0.924	0.442	0.272	1691	146
ISO_3	4.02-4.16	0.938	0.951	0.412	0.317	1730	168
ISO_3	3.9-4.02	0.919	0.907	0.38	0.287	1782	153
ISO_3	3.79-3.9	0.902	0.861	0.331	0.246	1831	160
ISO_3	3.68-3.79	0.901	0.906	0.328	0.216	1911	161
ISO_3	3.59-3.68	0.872	0.878	0.189	0.152	1933	151
ISO_3	3.5-3.59	0.865	0.881	0.272	0.188	2037	163
ANO_3	12.44-19.99	0.336	0	3.869	0	396	0
ANO_3	9.8-12.44	0.354	0	3.752	0	598	0
ANO_3	8.34-9.8	0.373	0	3.549	0	741	0
ANO_3	7.39-8.34	0.435	0	2.865	0	867	0
ANO_3	6.7-7.39	0.482	0	2.403	0	969	0
ANO_3	6.17-6.7	0.541	0	2.136	0	1079	0
ANO_3	5.75-6.17	0.597	0	1.914	0	1163	0
ANO_3	5.41-5.75	0.695	0	1.426	0	1264	0
ANO_3	5.12-5.41	0.717	0	1.303	0	1329	0
ANO_3	4.88-5.12	0.742	0	1.152	0	1416	0
ANO_3	4.66-4.88	0.784	0	0.986	0	1474	0
ANO_3	4.47-4.66	0.821	0	0.909	0	1523	0
ANO_3	4.31-4.47	0.867	0	0.727	0	1594	0
ANO_3	4.16-4.31	0.891	0	0.67	0	1691	0
ANO_3	4.02-4.16	0.923	0	0.557	0	1730	0
ANO_3	3.9-4.02	0.955	0	0.462	0	1783	0
ANO_3	3.79-3.9	0.966	0	0.39	0	1831	0
ANO_3	3.68-3.79	0.977	0	0.334	0	1911	0
ANO_3	3.59-3.68	0.988	0	0.285	0	1933	0
ANO_3	3.5-3.59	0.988	0	0.25	0	2037	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-158.348	-81.259	-203.119	SE	0	0.81
2	-101.733	-56.819	-200.195	SE	110.39	0.8
3	-181.125	-59.481	-201.783	SE	107.1	0.82
4	-171.684	-23.773	-211.47	SE	144.18	0.92
5	-171.589	-77.882	-205.625	SE	102.24	0.93
6	-173.592	-22.541	-199.086	SE	0	0.82
7	-173.139	24.166	-206.953	SE	0	0.95
8	-166.049	-90.135	-199.317	SE	0	0.89
9	-167.103	-9.677	-212.201	SE	138.1	0.96
10	-131.906	-67.529	-189.038	SE	100.93	0.85
11	-116.708	-56.543	-198.951	SE	133.08	0.83
12	-148.843	-88.494	-186.579	SE	118.9	0.96
13	-161.636	-80.547	-214.969	SE	111.55	0.6
14	-157.711	3.585	-197.83	SE	142.53	1.02
15	-111.469	-67.642	-196.329	SE	136.41	1.02
16	-94.186	52.539	-184.112	SE	122.1	0.76
17	-128.397	19.637	-201.878	SE	191.16	0.8
18	-122.458	33.366	-188.515	SE	124.81	0.47
19	-161.979	-16.449	-203.059	SE	140.94	0.85
20	-107.043	-49.024	-192.058	SE	129.12	0.85
21	-176.396	-79.608	-195.184	SE	132.97	0.83
22	-116.221	22.675	-196.868	SE	272.01	0.98
23	-72.88	-71.142	39.175	SE	0	0.92
24	-21.876	16.252	45.853	SE	161.36	0.62
25	-84.95	84.005	68.235	SE	145.41	0.54
26	-36.345	72.916	39.839	SE	149.1	0.3
27	13.255	172.1	27.909	SE	0	0.53
28	61.048	57.245	10.721	SE	128.16	0.42
29	58.433	55.27	13.078	SE	134.52	0.46
30	59.932	62.821	24.978	SE	135.15	0.39
31	23	159.1	18.884	SE	124.66	0.38
32	14.389	162.922	0	SE	133.23	0.3
33	85.73	171.807	4.944	SE	127.73	0.19
34	65.618	65.472	20.551	SE	0	0.16
35	-63.896	-55.825	59.741	SE	114.08	0.61
36	66.13	37.535	10.232	SE	1	0.16

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
12.44-19.99	0.924	0.676	408	145
9.8-12.44	0.898	0.671	601	149
8.34-9.8	0.874	0.631	741	154
7.39-8.34	0.848	0.634	867	135
6.7-7.39	0.837	0.58	969	145
6.17-6.7	0.821	0.521	1079	141
5.75-6.17	0.78	0.476	1163	150
5.41-5.75	0.721	0.476	1264	154
5.12-5.41	0.665	0.415	1329	155
4.88-5.12	0.638	0.386	1416	141
4.66-4.88	0.605	0.295	1474	150
4.47-4.66	0.56	0.278	1523	145
4.31-4.47	0.49	0.267	1594	146
4.16-4.31	0.458	0.184	1691	150
4.02-4.16	0.395	0.205	1730	168
3.9-4.02	0.334	0.216	1783	154
3.79-3.9	0.305	0.169	1831	160
3.68-3.79	0.253	0.125	1912	163
3.59-3.68	0.221	0.121	1934	151
3.5-3.59	0.185	0.099	2037	163

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
14.58-100	65.1	0.809	505
10.84-14.58	21.3	0.945	660
9.01-10.84	16.7	0.951	821
7.87-9.01	15.7	0.951	930
7.08-7.87	19.9	0.929	1054
6.49-7.08	20.5	0.919	1136
6.02-6.49	20.3	0.897	1226
5.65-6.02	20.3	0.881	1325
5.33-5.65	18.2	0.851	1391
5.06-5.33	18	0.855	1452
4.83-5.06	15.9	0.835	1527
4.63-4.83	14.9	0.841	1618
4.45-4.63	12.6	0.833	1661
4.29-4.45	14.3	0.795	1715
4.15-4.29	17.9	0.718	1785
4.02-4.15	13.7	0.732	1844
3.9-4.02	12.2	0.713	1893
3.79-3.9	10.6	0.699	1936
3.69-3.79	8.6	0.702	2018
3.6-3.69	7.9	0.681	2035
3.52-3.6	7.5	0.673	2085
3.44-3.52	6.6	0.663	2160
3.36-3.44	6.7	0.633	2188
3.29-3.36	5.2	0.632	2259
3.23-3.29	5.4	0.553	2278
3.16-3.23	5.2	0.547	2318
3.1-3.16	4.9	0.521	2382
3.05-3.1	5.8	0.469	2414
2.99-3.05	6.7	0.381	2814

Processing

Software

Name	Version	Classification	NB
SCALA	CCP4_3.1.20	data scaling
SHARP		phasing
DM	4.2	phasing
REFMAC	refmac_5.1.24	refinement
PDB_EXTRACT	1.502	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure: MAD / Resolution: 3→29.75 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.891 / SU B: 22.138 / SU ML: 0.402 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 4.532 / ESU R Free: 0.444 / Stereochemistry target values: Engh & Huber
Details: TLS refinement was necessary to obtain the best model. B factors were restrained across chains due to the use of TLS. Realistic B values should be derived from the TLS model.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.292	2458	5 %	RANDOM
Rwork	0.255	-	-	-
all	0.257	-	-	-
obs	-	48826	100 %	-

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

Displacement parameters

B_iso mean: 40.457 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.04 Å2	0 Å2	0 Å2
2-	-	0.04 Å2	0 Å2
3-	-	-	-0.07 Å2

Refinement step

Cycle: LAST / Resolution: 3→29.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11290	0	208	9	11507

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	11761
X-RAY DIFFRACTION	r_angle_refined_deg	0.917	1.962	15961
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.658	5	1432
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1794
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8904
X-RAY DIFFRACTION	r_nbd_refined	0.151	0.3	4925
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.5	459
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.145	0.3	114
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.335	0.5	8
X-RAY DIFFRACTION	r_mcbond_it	0.067	1.5	7251
X-RAY DIFFRACTION	r_mcangle_it	0.127	2	11635
X-RAY DIFFRACTION	r_scbond_it	0.233	3	4510
X-RAY DIFFRACTION	r_scangle_it	0.36	4.5	4326

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	1119	MEDIUM POSITIONAL	0.51	0.5
1	2	B	1119	MEDIUM POSITIONAL	0.46	0.5
1	3	C	1119	MEDIUM POSITIONAL	0.38	0.5
1	4	D	1119	MEDIUM POSITIONAL	0.36	0.5
1	5	E	1119	MEDIUM POSITIONAL	0.36	0.5
1	6	F	1119	MEDIUM POSITIONAL	0.41	0.5
1	7	G	1119	MEDIUM POSITIONAL	0.36	0.5
1	8	H	1119	MEDIUM POSITIONAL	0.38	0.5
1	1	A	1119	MEDIUM THERMAL	0.19	2
1	2	B	1119	MEDIUM THERMAL	0.17	2
1	3	C	1119	MEDIUM THERMAL	0.12	2
1	4	D	1119	MEDIUM THERMAL	0.11	2
1	5	E	1119	MEDIUM THERMAL	0.12	2
1	6	F	1119	MEDIUM THERMAL	0.19	2
1	7	G	1119	MEDIUM THERMAL	0.12	2
1	8	H	1119	MEDIUM THERMAL	0.14	2
2	1	A	217	MEDIUM POSITIONAL	0.52	0.5
2	2	D	217	MEDIUM POSITIONAL	0.44	0.5
2	3	E	217	MEDIUM POSITIONAL	0.74	0.5
2	4	H	217	MEDIUM POSITIONAL	0.46	0.5
2	1	A	217	MEDIUM THERMAL	0.25	2
2	2	D	217	MEDIUM THERMAL	0.12	2
2	3	E	217	MEDIUM THERMAL	0.14	2
2	4	H	217	MEDIUM THERMAL	0.17	2
3	1	B	199	MEDIUM POSITIONAL	0.58	0.5
3	2	C	199	MEDIUM POSITIONAL	0.45	0.5
3	3	F	199	MEDIUM POSITIONAL	0.46	0.5
3	4	G	199	MEDIUM POSITIONAL	0.58	0.5
3	1	B	199	MEDIUM THERMAL	0.16	2
3	2	C	199	MEDIUM THERMAL	0.11	2
3	3	F	199	MEDIUM THERMAL	0.14	2
3	4	G	199	MEDIUM THERMAL	0.16	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Rfactor all	Num. reflection all
3-3.0771	0.331	181	0.283	3335	0.285	3516
3.077-3.1605	0.288	174	0.273	3281	0.273	3455
3.161-3.2511	0.331	141	0.304	3194	0.305	3335
3.251-3.3499	0.343	167	0.293	3093	0.296	3260
3.35-3.4583	0.326	178	0.296	2990	0.298	3168
3.458-3.5779	0.347	177	0.281	2892	0.285	3069
3.578-3.7109	0.336	145	0.292	2812	0.294	2957
3.711-3.8599	0.309	124	0.272	2725	0.274	2849
3.86-4.0285	0.312	150	0.262	2620	0.265	2770
4.028-4.2213	0.282	122	0.246	2492	0.247	2614
4.221-4.4446	0.29	136	0.233	2369	0.236	2505
4.445-4.7077	0.244	122	0.211	2276	0.213	2398
4.708-5.0237	0.251	113	0.222	2125	0.224	2238
5.024-5.4134	0.334	104	0.261	2009	0.265	2113
5.413-5.9105	0.329	104	0.286	1851	0.289	1955
5.911-6.5758	0.304	100	0.267	1696	0.269	1796
6.576-7.532	0.247	70	0.248	1512	0.248	1582
7.532-9.0804	0.261	77	0.204	1302	0.207	1379
9.08-12.2822	0.166	42	0.2	1079	0.199	1121
12.282-29.748	0.365	31	0.345	715	0.346	746

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.2957	-0.0048	1.2198	3.4353	-1.2236	7.3832	0.2714	0.0893	0.1581	0.0404	0.1313	0.3106	0.2533	-0.4911	-0.4027	0.1153	-0.0068	0.0873	0.1057	0.1379	0.2889	5.0794	155.1559	20.9183
2	6.7545	0.305	-1.2175	2.5972	0.9803	5.4317	0.1148	-0.0738	0.2187	-0.0621	0.1035	0.1716	-0.7183	0.241	-0.2183	0.3878	-0.0692	0.201	0.0599	0.0427	0.2338	21.9116	178.0263	15.071
3	6.4641	-0.9914	3.1719	4.0397	-2.4747	6.81	0.5407	-0.2533	-0.454	-0.0065	-0.8801	0.0947	0.9009	-0.3483	0.3394	0.5751	-0.1232	-0.0277	0.395	-0.0579	0.3431	87.131	160.7691	11.687
4	5.1207	2.1144	-0.7396	7.5127	-0.2011	4.5415	0.3845	-0.4016	0.321	0.1618	-0.8516	1.1227	0.1324	-0.7884	0.4671	0.3641	0.0525	0.0132	0.7524	-0.6055	0.7179	67.5969	183.0602	10.079
5	4.7841	-0.3097	-0.1344	4.1475	-1.7789	7.0647	0.1448	0.102	-0.0026	-0.3733	-0.1051	-0.2656	0.5291	0.9573	-0.0397	0.5273	0.403	-0.1629	0.4967	-0.2075	0.3803	39.1971	96.4957	26.0596
6	2.6856	-0.3038	-1.0323	5.9297	2.7958	4.6737	0.415	0.3458	-0.0979	-0.6694	0.0409	-0.3606	-0.2317	0.5885	-0.4559	0.381	0.0404	-0.0225	0.1902	-0.072	0.1683	25.4126	122.777	21.5956
7	2.635	0.6095	2.1465	2.3918	-1.1806	4.2884	0.3213	0.4872	0.2832	-0.8334	-0.9751	0.9304	-0.3944	-0.2683	0.6538	1.082	0.5025	-0.4821	1.0305	-0.7289	1.0583	67.3124	67.9256	32.3149
8	4.328	-1.1444	-0.5122	5.2021	-0.746	3.5686	-0.0277	0.4251	0.4904	-0.7663	-1.1958	0.9931	-0.3253	-0.6399	1.2234	1.2966	0.6039	-0.5232	1.0662	-0.8788	1.0141	65.3405	44.2219	12.6106

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	-1 - 109	1 - 111
2	1	A	A	114 - 190	116 - 192
3	1	A	I	400
4	2	B	B	2 - 190	4 - 192
5	2	B	J	401
6	3	C	C	2 - 185	4 - 187
7	3	C	K	402
8	4	D	D	2 - 104	4 - 106
9	4	D	D	114 - 191	116 - 193
10	4	D	L	403
11	5	E	E	2 - 104	4 - 106
12	5	E	E	114 - 191	116 - 193
13	5	E	M	404
14	6	F	F	2 - 185	4 - 187
15	6	F	N	405
16	7	G	G	5 - 9	7 - 11
17	7	G	G	12 - 101	14 - 103
18	7	G	G	106 - 110	108 - 112
19	7	G	O	406
20	7	G	G	112 - 185	114 - 187
21	8	H	H	4 - 10	6 - 12
22	8	H	H	70 - 87	72 - 89
23	8	H	H	91 - 103	93 - 105
24	8	H	H	114 - 190	116 - 192
25	8	H	P	407
26	8	H	H	12 - 54	14 - 56
27	8	H	H	57 - 68	59 - 70