PDB-2a7k: carboxymethylproline synthase (CarB) from pectobacterium carotovo...

ID or keywords:

Entry

Database: PDB / ID: 2a7k

Title

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

Components

CarB

Keywords

BIOSYNTHETIC PROTEIN /

carbapenem /

carbapenam /

crotonase /

antibiotic /

beta-lactam

Function / homology

Function and homology information

carboxymethylproline synthase / antibiotic biosynthetic process /

transferase activity
Similarity search - Function

Biological species

Pectobacterium carotovorum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.24 Å

Authors

Sleeman, M.C. / Sorensen, J.L. / Batchelar, E.T. / McDonough, M.A. / Schofield, C.J.

Citation

Journal: J.Biol.Chem. / Year: 2005
Title: Structural and Mechanistic Studies on Carboxymethylproline Synthase (CarB), a Unique Member of the Crotonase Superfamily Catalyzing the First Step in Carbapenem Biosynthesis.
Authors: Sleeman, M.C. / Sorensen, J.L. / Batchelar, E.T. / McDonough, M.A. / Schofield, C.J.

History

Deposition	Jul 5, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2a7k.cif.gz	804.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2a7k.ent.gz	672.2 KB	Display	PDB format
PDBx/mmJSON format	2a7k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a7/2a7k ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a7k	HTTPS FTP

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Related structure data

Related structure data	2a81C C: citing same article (ref.)
Similar structure data	2a81-d 5u8o-1 3l3s-1 4jjt-d 4hc8-1 4zgu-d 1i7l-d 5xnc-2 4qyp-d 4fn7-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2a81C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CarB

B: CarB

C: CarB

D: CarB

E: CarB

F: CarB

G: CarB

H: CarB

I: CarB

248 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CarB

B: CarB

C: CarB

defined by author&software
82.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: CarB

E: CarB

F: CarB

defined by author&software
82.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: CarB

H: CarB

I: CarB

defined by author&software
82.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.207, 89.860, 264.582
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ASN	ASN	2	C	C	1 - 19	1 - 19
2	1	MET	MET	ASN	ASN	2	A	A	1 - 19	1 - 19
3	1	MET	MET	ASN	ASN	2	B	B	1 - 19	1 - 19
4	1	MET	MET	ASN	ASN	2	D	D	1 - 19	1 - 19
5	1	MET	MET	ASN	ASN	2	E	E	1 - 19	1 - 19
6	1	MET	MET	ASN	ASN	2	F	F	1 - 19	1 - 19
7	1	MET	MET	ASN	ASN	2	G	G	1 - 19	1 - 19
8	1	MET	MET	ASN	ASN	2	H	H	1 - 19	1 - 19
9	1	MET	MET	ASN	ASN	2	I	I	1 - 19	1 - 19
10	2	LYS	LYS	LYS	LYS	3	C	C	20	20
11	2	LYS	LYS	LYS	LYS	3	A	A	20	20
12	2	LYS	LYS	LYS	LYS	3	B	B	20	20
13	2	LYS	LYS	LYS	LYS	3	D	D	20	20
14	2	LYS	LYS	LYS	LYS	3	E	E	20	20
15	2	LYS	LYS	LYS	LYS	3	F	F	20	20
16	2	LYS	LYS	LYS	LYS	3	G	G	20	20
17	2	LYS	LYS	LYS	LYS	3	H	H	20	20
18	2	LYS	LYS	LYS	LYS	3	I	I	20	20
19	3	HIS	HIS	VAL	VAL	2	C	C	21 - 45	21 - 45
20	3	HIS	HIS	VAL	VAL	2	A	A	21 - 45	21 - 45
21	3	HIS	HIS	VAL	VAL	2	B	B	21 - 45	21 - 45
22	3	HIS	HIS	VAL	VAL	2	D	D	21 - 45	21 - 45
23	3	HIS	HIS	VAL	VAL	2	E	E	21 - 45	21 - 45
24	3	HIS	HIS	VAL	VAL	2	F	F	21 - 45	21 - 45
25	3	HIS	HIS	VAL	VAL	2	G	G	21 - 45	21 - 45
26	3	HIS	HIS	VAL	VAL	2	H	H	21 - 45	21 - 45
27	3	HIS	HIS	VAL	VAL	2	I	I	21 - 45	21 - 45
28	4	ARG	ARG	ARG	ARG	3	C	C	46	46
29	4	ARG	ARG	ARG	ARG	3	A	A	46	46
30	4	ARG	ARG	ARG	ARG	3	B	B	46	46
31	4	ARG	ARG	ARG	ARG	3	D	D	46	46
32	4	ARG	ARG	ARG	ARG	3	E	E	46	46
33	4	ARG	ARG	ARG	ARG	3	F	F	46	46
34	4	ARG	ARG	ARG	ARG	3	G	G	46	46
35	4	ARG	ARG	ARG	ARG	3	H	H	46	46
36	4	ARG	ARG	ARG	ARG	3	I	I	46	46
37	5	ALA	ALA	ASP	ASP	2	C	C	47 - 63	47 - 63
38	5	ALA	ALA	ASP	ASP	2	A	A	47 - 63	47 - 63
39	5	ALA	ALA	ASP	ASP	2	B	B	47 - 63	47 - 63
40	5	ALA	ALA	ASP	ASP	2	D	D	47 - 63	47 - 63
41	5	ALA	ALA	ASP	ASP	2	E	E	47 - 63	47 - 63
42	5	ALA	ALA	ASP	ASP	2	F	F	47 - 63	47 - 63
43	5	ALA	ALA	ASP	ASP	2	G	G	47 - 63	47 - 63
44	5	ALA	ALA	ASP	ASP	2	H	H	47 - 63	47 - 63
45	5	ALA	ALA	ASP	ASP	2	I	I	47 - 63	47 - 63
46	6	PHE	PHE	GLU	GLU	6	C	C	64 - 78	64 - 78
47	6	PHE	PHE	GLU	GLU	6	A	A	64 - 78	64 - 78
48	6	PHE	PHE	GLU	GLU	6	B	B	64 - 78	64 - 78
49	6	PHE	PHE	GLU	GLU	6	D	D	64 - 78	64 - 78
50	6	PHE	PHE	GLU	GLU	6	E	E	64 - 78	64 - 78
51	6	PHE	PHE	GLU	GLU	6	F	F	64 - 78	64 - 78
52	6	ASP	ASP	GLU	GLU	6	G	G	63 - 78	63 - 78
53	6	PHE	PHE	GLU	GLU	6	H	H	64 - 78	64 - 78
54	6	PHE	PHE	GLU	GLU	6	I	I	64 - 78	64 - 78
55	7	TRP	TRP	ALA	ALA	2	C	C	79 - 105	79 - 105
56	7	TRP	TRP	ALA	ALA	2	A	A	79 - 105	79 - 105
57	7	TRP	TRP	ALA	ALA	2	B	B	79 - 105	79 - 105
58	7	TRP	TRP	ALA	ALA	2	D	D	79 - 105	79 - 105
59	7	TRP	TRP	ALA	ALA	2	E	E	79 - 105	79 - 105
60	7	TRP	TRP	ALA	ALA	2	F	F	79 - 105	79 - 105
61	7	TRP	TRP	ALA	ALA	2	G	G	79 - 105	79 - 105
62	7	TRP	TRP	ALA	ALA	2	H	H	79 - 105	79 - 105
63	7	TRP	TRP	ALA	ALA	2	I	I	79 - 105	79 - 105
64	8	ILE	ILE	ILE	ILE	3	C	C	106	106
65	8	ILE	ILE	ILE	ILE	3	A	A	106	106
66	8	ILE	ILE	ILE	ILE	3	B	B	106	106
67	8	ILE	ILE	ILE	ILE	3	D	D	106	106
68	8	ILE	ILE	ILE	ILE	3	E	E	106	106
69	8	ILE	ILE	ILE	ILE	3	F	F	106	106
70	8	ILE	ILE	ILE	ILE	3	G	G	106	106
71	8	ILE	ILE	ILE	ILE	3	H	H	106	106
72	8	ILE	ILE	ILE	ILE	3	I	I	106	106
73	9	GLY	GLY	ILE	ILE	2	C	C	107 - 157	107 - 157
74	9	GLY	GLY	ILE	ILE	2	A	A	107 - 157	107 - 157
75	9	GLY	GLY	ILE	ILE	2	B	B	107 - 157	107 - 157
76	9	GLY	GLY	ILE	ILE	2	D	D	107 - 157	107 - 157
77	9	GLY	GLY	ILE	ILE	2	E	E	107 - 157	107 - 157
78	9	GLY	GLY	ILE	ILE	2	F	F	107 - 157	107 - 157
79	9	GLY	GLY	ILE	ILE	2	G	G	107 - 157	107 - 157
80	9	GLY	GLY	ILE	ILE	2	H	H	107 - 157	107 - 157
81	9	GLY	GLY	ILE	ILE	2	I	I	107 - 157	107 - 157
82	10	ILE	ILE	ILE	ILE	3	C	C	158	158
83	10	ILE	ILE	ILE	ILE	3	A	A	158	158
84	10	ILE	ILE	ILE	ILE	3	B	B	158	158
85	10	ILE	ILE	ILE	ILE	3	D	D	158	158
86	10	ILE	ILE	ILE	ILE	3	E	E	158	158
87	10	ILE	ILE	ILE	ILE	3	F	F	158	158
88	10	ILE	ILE	ILE	ILE	3	G	G	158	158
89	10	ILE	ILE	ILE	ILE	3	H	H	158	158
90	10	ILE	ILE	ILE	ILE	3	I	I	158	158
91	11	TYR	TYR	THR	THR	2	C	C	159 - 190	159 - 190
92	11	TYR	TYR	THR	THR	2	A	A	159 - 190	159 - 190
93	11	TYR	TYR	THR	THR	2	B	B	159 - 190	159 - 190
94	11	TYR	TYR	THR	THR	2	D	D	159 - 190	159 - 190
95	11	TYR	TYR	THR	THR	2	E	E	159 - 190	159 - 190
96	11	TYR	TYR	THR	THR	2	F	F	159 - 190	159 - 190
97	11	TYR	TYR	THR	THR	2	G	G	159 - 190	159 - 190
98	11	TYR	TYR	THR	THR	2	H	H	159 - 190	159 - 190
99	11	TYR	TYR	THR	THR	2	I	I	159 - 190	159 - 190
100	12	GLN	GLN	GLN	GLN	3	C	C	191	191
101	12	GLN	GLN	GLN	GLN	3	A	A	191	191
102	12	GLN	GLN	GLN	GLN	3	B	B	191	191
103	12	GLN	GLN	GLN	GLN	3	D	D	191	191
104	12	GLN	GLN	GLN	GLN	3	E	E	191	191
105	12	GLN	GLN	GLN	GLN	3	F	F	191	191
106	12	GLN	GLN	GLN	GLN	3	G	G	191	191
107	12	GLN	GLN	GLN	GLN	3	H	H	191	191
108	12	GLN	GLN	GLN	GLN	3	I	I	191	191
109	13	ALA	ALA	LYS	LYS	2	C	C	192 - 207	192 - 207
110	13	ALA	ALA	LYS	LYS	2	A	A	192 - 207	192 - 207
111	13	ALA	ALA	LYS	LYS	2	B	B	192 - 207	192 - 207
112	13	ALA	ALA	LYS	LYS	2	D	D	192 - 207	192 - 207
113	13	ALA	ALA	LYS	LYS	2	E	E	192 - 207	192 - 207
114	13	ALA	ALA	LYS	LYS	2	F	F	192 - 207	192 - 207
115	13	ALA	ALA	LYS	LYS	2	G	G	192 - 207	192 - 207
116	13	ALA	ALA	LYS	LYS	2	H	H	192 - 207	192 - 207
117	13	ALA	ALA	LYS	LYS	2	I	I	192 - 207	192 - 207
118	14	ARG	ARG	ARG	ARG	3	C	C	208	208
119	14	ARG	ARG	ARG	ARG	3	A	A	208	208
120	14	ARG	ARG	ARG	ARG	3	B	B	208	208
121	14	ARG	ARG	ARG	ARG	3	D	D	208	208
122	14	ARG	ARG	ARG	ARG	3	E	E	208	208
123	14	ARG	ARG	ARG	ARG	3	F	F	208	208
124	14	ARG	ARG	ARG	ARG	3	G	G	208	208
125	14	ARG	ARG	ARG	ARG	3	H	H	208	208
126	14	ARG	ARG	ARG	ARG	3	I	I	208	208
127	15	ALA	ALA	ILE	ILE	2	C	C	209 - 215	209 - 215
128	15	ALA	ALA	ILE	ILE	2	A	A	209 - 215	209 - 215
129	15	ALA	ALA	ILE	ILE	2	B	B	209 - 215	209 - 215
130	15	ALA	ALA	ILE	ILE	2	D	D	209 - 215	209 - 215
131	15	ALA	ALA	ILE	ILE	2	E	E	209 - 215	209 - 215
132	15	ALA	ALA	ILE	ILE	2	F	F	209 - 215	209 - 215
133	15	ALA	ALA	ILE	ILE	2	G	G	209 - 215	209 - 215
134	15	ALA	ALA	ILE	ILE	2	H	H	209 - 215	209 - 215
135	15	ALA	ALA	ILE	ILE	2	I	I	209 - 215	209 - 215
136	16	HIS	HIS	HIS	HIS	3	C	C	216	216
137	16	HIS	HIS	HIS	HIS	3	A	A	216	216
138	16	HIS	HIS	HIS	HIS	3	B	B	216	216
139	16	HIS	HIS	HIS	HIS	3	D	D	216	216
140	16	HIS	HIS	HIS	HIS	3	E	E	216	216
141	16	HIS	HIS	HIS	HIS	3	F	F	216	216
142	16	HIS	HIS	HIS	HIS	3	G	G	216	216
143	16	HIS	HIS	HIS	HIS	3	H	H	216	216
144	16	HIS	HIS	HIS	HIS	3	I	I	216	216
145	17	LEU	LEU	GLU	GLU	2	C	C	217 - 219	217 - 219
146	17	LEU	LEU	GLU	GLU	2	A	A	217 - 219	217 - 219
147	17	LEU	LEU	GLU	GLU	2	B	B	217 - 219	217 - 219
148	17	LEU	LEU	GLU	GLU	2	D	D	217 - 219	217 - 219
149	17	LEU	LEU	GLU	GLU	2	E	E	217 - 219	217 - 219
150	17	LEU	LEU	GLU	GLU	2	F	F	217 - 219	217 - 219
151	17	LEU	LEU	GLU	GLU	2	G	G	217 - 219	217 - 219
152	17	LEU	LEU	GLU	GLU	2	H	H	217 - 219	217 - 219
153	17	LEU	LEU	GLU	GLU	2	I	I	217 - 219	217 - 219
154	18	GLN	GLN	GLN	GLN	3	C	C	220	220
155	18	GLN	GLN	GLN	GLN	3	A	A	220	220
156	18	GLN	GLN	GLN	GLN	3	B	B	220	220
157	18	GLN	GLN	GLN	GLN	3	D	D	220	220
158	18	GLN	GLN	GLN	GLN	3	E	E	220	220
159	18	GLN	GLN	GLN	GLN	3	F	F	220	220
160	18	GLN	GLN	GLN	GLN	3	G	G	220	220
161	18	GLN	GLN	GLN	GLN	3	H	H	220	220
162	18	GLN	GLN	GLN	GLN	3	I	I	220	220
163	19	THR	THR	SER	SER	2	C	C	221 - 225	221 - 225
164	19	THR	THR	SER	SER	2	A	A	221 - 225	221 - 225
165	19	THR	THR	SER	SER	2	B	B	221 - 225	221 - 225
166	19	THR	THR	SER	SER	2	D	D	221 - 225	221 - 225
167	19	THR	THR	SER	SER	2	E	E	221 - 225	221 - 225
168	19	THR	THR	SER	SER	2	F	F	221 - 225	221 - 225
169	19	THR	THR	SER	SER	2	G	G	221 - 225	221 - 225
170	19	THR	THR	SER	SER	2	H	H	221 - 225	221 - 225
171	19	THR	THR	SER	SER	2	I	I	221 - 225	221 - 225
172	20	LYS	LYS	ALA	ALA	6	C	C	226 - 238	226 - 238
173	20	LYS	LYS	LYS	LYS	6	A	A	226 - 230	226 - 230
174	20	LYS	LYS	LYS	LYS	6	B	B	226 - 230	226 - 230
175	20	LYS	LYS	LYS	LYS	6	D	D	226 - 230	226 - 230
176	20	LYS	LYS	ARG	ARG	6	E	E	226 - 236	226 - 236
177	20	LYS	LYS	LYS	LYS	6	F	F	226	226
178	20	LYS	LYS	LYS	LYS	6	G	G	226 - 230	226 - 230
179	20	LYS	LYS	ALA	ALA	6	H	H	226 - 231	226 - 231
180	20	LYS	LYS	HIS	HIS	6	I	I	226 - 229	226 - 229

Details

The biological unit is a trimer. There are 3 biological units in the asymmetric unit (chains A, B & C, chains D, E & F and chains G, H & I)

#1: Protein	CarB Mass: 27608.275 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: CarB / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XB60
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CarB

Mass: 27608.275 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pectobacterium carotovorum (bacteria) / Gene: CarB / Plasmid: pET24a / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XB60

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, MgCl2, HEPES.Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SRS	PX14.2	1	0.978
SYNCHROTRON	SRS	PX10.1	2	0.9801, 0.98033, 0.976071

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 4	1	CCD	Jul 7, 2004	mirrors
MARMOSAIC 225 mm CCD	2	CCD	Sep 24, 2004	mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	si 111	SINGLE WAVELENGTH	M	x-ray	1
2	si 111	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.978	1
2	0.9801	1
3	0.98033	1
4	0.976071	1

Reflection

Number: 73417 / R_merge(I) obs: 0.096 / Χ²: 1.046 / D res high: 2.5 Å / D res low: 50 Å / % possible obs: 99.9 / Redundancy: 6.7 %

ID
1
2
3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.38	50	99.7	1	0.073	1.087	6.8
4.27	5.38	99.9	1	0.08	1.083	6.8
3.73	4.27	100	1	0.072	1.08	6.8
3.39	3.73	100	1	0.089	1.089	6.9
3.15	3.39	100	1	0.118	1.067	6.8
2.96	3.15	100	1	0.165	1.091	6.8
2.82	2.96	100	1	0.224	1.063	6.8
2.69	2.82	100	1	0.292	0.999	6.8
2.59	2.69	100	1	0.404	0.957	6.7
2.5	2.59	99.8	1	0.545	0.918	6.1
5.38	50	99.7	2	0.073	1.087	6.8
4.27	5.38	99.9	2	0.08	1.083	6.8
3.73	4.27	100	2	0.072	1.08	6.8
3.39	3.73	100	2	0.089	1.089	6.9
3.15	3.39	100	2	0.118	1.067	6.8
2.96	3.15	100	2	0.165	1.091	6.8
2.82	2.96	100	2	0.224	1.063	6.8
2.69	2.82	100	2	0.292	0.999	6.8
2.59	2.69	100	2	0.404	0.957	6.7
2.5	2.59	99.8	2	0.545	0.918	6.1
5.38	50	99.7	3	0.073	1.087	6.8
4.27	5.38	99.9	3	0.08	1.083	6.8
3.73	4.27	100	3	0.072	1.08	6.8
3.39	3.73	100	3	0.089	1.089	6.9
3.15	3.39	100	3	0.118	1.067	6.8
2.96	3.15	100	3	0.165	1.091	6.8
2.82	2.96	100	3	0.224	1.063	6.8
2.69	2.82	100	3	0.292	0.999	6.8
2.59	2.69	100	3	0.404	0.957	6.7
2.5	2.59	99.8	3	0.545	0.918	6.1

Reflection

Resolution: 2.1→52.93 Å / Num. obs: 100581 / % possible obs: 99.8 % / Redundancy: 4.3 % / B_iso Wilson estimate: 36 Å² / R_merge(I) obs: 0.088 / R_sym value: 0.088 / Net I/σ(I): 5.7

Reflection shell

Resolution: 2.24→2.36 Å / % possible obs: 99.6 % / Redundancy: 3.1 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 14507 / Num. unique all: 14507 / R_sym value: 0.35 / % possible all: 99.6

-
Phasing

Phasing

Method:

MAD

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	61.652	1.29	32.485	S	20	1
2	69.787	-0.072	76.786	S	20	0.999
3	60.02	3.945	120.685	S	20	0.957
4	50.976	15.075	126.248	S	20	0.922
5	65.554	42.048	78.05	S	20	0.916
6	42.013	17.717	113.229	S	20	0.914
7	22.322	-0.73	99.134	S	20	0.903
8	53.059	25.554	89.593	S	20	0.896
9	51.85	12.571	37.253	S	20	0.883
10	57.368	37.822	80.594	S	20	0.848
11	42.438	9.703	47.978	S	20	0.847
12	-0.001	-10.94	93.409	S	20	0.837
13	10.952	4.599	86.941	S	20	0.835
14	30.162	5.643	141.516	S	20	0.826
15	-4.271	17.939	83.71	S	20	0.823
16	-9.618	-12.749	82.02	S	20	0.821
17	41.032	11.343	60.135	S	20	0.818
18	46.132	21.187	25.863	S	20	0.806
19	21.698	-1.432	144.909	S	20	0.803
20	12.763	15.539	86.224	S	20	0.79
21	1.401	-11.04	105.291	S	20	0.772
22	41.896	12.463	149.908	S	20	0.772
23	61.33	5.742	137.496	S	20	0.77
24	53.476	37.111	89.184	S	20	0.769
25	32.918	-17.056	131.384	S	20	0.769
26	14.779	4.383	95.905	S	20	0.768
27	-0.672	11.581	65.619	S	20	0.763
28	36.08	26.747	91.433	S	20	0.76
29	13.268	-6.278	96.237	S	20	0.759
30	32.884	-5.371	132.465	S	20	0.747
31	81.471	-0.202	77.266	S	20	0.747
32	48.395	1.661	121.995	S	20	0.741
33	4.709	5.247	105.59	S	20	0.728
34	42.682	33.861	22.118	S	20	0.713
35	69.706	-2.865	93.851	S	20	0.707
36	49.774	-1.022	33.25	S	20	0.704
37	42.281	11.253	137.972	S	20	0.699
38	30.027	-5.501	141.142	S	20	0.692
39	57.253	49.024	81.495	S	20	0.684
40	49.601	-16.595	128.649	S	20	0.678
41	54.443	23.857	133.048	S	20	0.676
42	61.257	4.681	49.256	S	20	0.675
43	40.643	-5.18	150.064	S	20	0.674
44	40.055	30.483	110.196	S	20	0.674
45	47.782	33.34	102.011	S	20	0.668
46	81.988	8.27	73.731	S	20	0.667
47	49.751	36.857	13.062	S	20	0.666
48	93.372	8.23	74.596	S	20	0.654
49	47.402	39.427	71.3	S	20	0.634
50	51.105	15.567	137.785	S	20	0.615
51	38.377	37.795	14.463	S	20	0.593
52	50.521	-9.941	30.208	S	20	0.592
53	26.845	-4.124	110.89	S	20	0.589
54	-13.292	-20.877	89.14	S	20	0.58
55	54.028	22.205	43.512	S	20	0.564
56	-9.096	-13.856	93.369	S	20	0.538
57	70.474	45.926	66.194	S	20	0.499
58	66.261	28.994	129.285	S	20	0.474
59	50.809	14.606	48.648	S	20	0.449

Phasing dm

FOM : 0.74 / FOM acentric: 0.74 / FOM centric: 0.67 / Reflection: 92973 / Reflection acentric: 85089 / Reflection centric: 7884

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.6-45.466	0.92	0.91	0.93	4104	3240	864
4.1-6.6	0.89	0.9	0.84	12573	11068	1505
3.3-4.1	0.85	0.86	0.79	15618	14206	1412
2.9-3.3	0.74	0.75	0.63	15708	14495	1213
2.5-2.9	0.65	0.66	0.49	27780	25922	1858
2.3-2.5	0.61	0.62	0.41	17190	16158	1032

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
SHELX		phasing
RESOLVE	2.08	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
MOSFLM		data reduction
HKL-2000		data reduction
CCP4	(SCALA)	data scaling
SCALEPACK		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.24→45.596 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.918 / WR_factor R_free: 0.234 / WR_factor R_work: 0.182 / SU B: 13.989 / SU ML: 0.18 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.228 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2385	5084	5.061 %	random
R_work	0.1849	-	-	-
all	0.188	-	-	-
obs	0.188	100449	99.673 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.784 Å²	0 Å²	0 Å²
2-	-	-0.779 Å²	0 Å²
3-	-	-	-0.005 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→45.596 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15898	0	0	806	16704

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	16189
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14638
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.936	21947
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	33895
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.936	5	2061
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.924	24.331	762
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.908	15	2628
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.293	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	2509
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	18353
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3318
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.3	3769
X-RAY DIFFRACTION	r_nbd_other	0.195	0.3	15220
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.5	8048
X-RAY DIFFRACTION	r_nbtor_other	0.096	0.5	9765
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.5	1633
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.151	0.5	3
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.185	0.3	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.283	0.3	83
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.25	0.5	24
X-RAY DIFFRACTION	r_mcbond_it	0.593	1.5	10973
X-RAY DIFFRACTION	r_mcbond_other	0.204	1.5	4211
X-RAY DIFFRACTION	r_mcangle_it	0.859	2	16533
X-RAY DIFFRACTION	r_mcangle_other	0.405	2	14282
X-RAY DIFFRACTION	r_scbond_it	1.644	3	6311
X-RAY DIFFRACTION	r_scbond_other	0.658	3	12369
X-RAY DIFFRACTION	r_scangle_it	2.497	4.5	5414
X-RAY DIFFRACTION	r_scangle_other	0.997	4.5	19613

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Rms	Type	Weight
1	C	1216	0.06	TIGHT POSITIONAL	0.05
2	A	1216	0.05	TIGHT POSITIONAL	0.05
3	B	1216	0.06	TIGHT POSITIONAL	0.05
4	D	1216	0.07	TIGHT POSITIONAL	0.05
5	E	1216	0.05	TIGHT POSITIONAL	0.05
6	F	1216	0.05	TIGHT POSITIONAL	0.05
7	G	1216	0.05	TIGHT POSITIONAL	0.05
8	H	1216	0.06	TIGHT POSITIONAL	0.05
9	I	1216	0.06	TIGHT POSITIONAL	0.05
1	C	1726	0.35	MEDIUM POSITIONAL	0.5
2	A	1726	0.46	MEDIUM POSITIONAL	0.5
3	B	1726	0.4	MEDIUM POSITIONAL	0.5
4	D	1726	0.49	MEDIUM POSITIONAL	0.5
5	E	1726	0.38	MEDIUM POSITIONAL	0.5
6	F	1726	0.47	MEDIUM POSITIONAL	0.5
7	G	1726	0.38	MEDIUM POSITIONAL	0.5
8	H	1726	0.42	MEDIUM POSITIONAL	0.5
9	I	1726	0.44	MEDIUM POSITIONAL	0.5
1	C	174	1.42	LOOSE POSITIONAL	5
2	A	174	1.06	LOOSE POSITIONAL	5
3	B	174	1.12	LOOSE POSITIONAL	5
4	D	174	1.18	LOOSE POSITIONAL	5
5	E	174	0.99	LOOSE POSITIONAL	5
6	F	174	1.03	LOOSE POSITIONAL	5
7	G	174	1.11	LOOSE POSITIONAL	5
8	H	174	0.94	LOOSE POSITIONAL	5
9	I	174	1.18	LOOSE POSITIONAL	5
1	C	1216	0.13	TIGHT THERMAL	0.5
2	A	1216	0.12	TIGHT THERMAL	0.5
3	B	1216	0.13	TIGHT THERMAL	0.5
4	D	1216	0.15	TIGHT THERMAL	0.5
5	E	1216	0.13	TIGHT THERMAL	0.5
6	F	1216	0.12	TIGHT THERMAL	0.5
7	G	1216	0.12	TIGHT THERMAL	0.5
8	H	1216	0.12	TIGHT THERMAL	0.5
9	I	1216	0.13	TIGHT THERMAL	0.5
1	C	1726	0.6	MEDIUM THERMAL	2
2	A	1726	0.58	MEDIUM THERMAL	2
3	B	1726	0.68	MEDIUM THERMAL	2
4	D	1726	0.69	MEDIUM THERMAL	2
5	E	1726	0.53	MEDIUM THERMAL	2
6	F	1726	0.58	MEDIUM THERMAL	2
7	G	1726	0.59	MEDIUM THERMAL	2
8	H	1726	0.56	MEDIUM THERMAL	2
9	I	1726	0.57	MEDIUM THERMAL	2
1	C	174	3.81	LOOSE THERMAL	10
2	A	174	2.23	LOOSE THERMAL	10
3	B	174	3.28	LOOSE THERMAL	10
4	D	174	3	LOOSE THERMAL	10
5	E	174	2.63	LOOSE THERMAL	10
6	F	174	3.69	LOOSE THERMAL	10
7	G	174	2.01	LOOSE THERMAL	10
8	H	174	1.11	LOOSE THERMAL	10
9	I	174	3.79	LOOSE THERMAL	10

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.24-2.298	0.424	344	0.328	6885	7339	98.501
2.298-2.361	0.272	347	0.234	6840	7200	99.819
2.361-2.429	0.253	331	0.224	6607	6940	99.971
2.429-2.504	0.259	333	0.216	6443	6776	100
2.504-2.585	0.252	336	0.205	6219	6555	100
2.585-2.676	0.266	360	0.201	5998	6358	100
2.676-2.777	0.28	293	0.199	5864	6157	100
2.777-2.89	0.244	323	0.194	5627	5950	100
2.89-3.017	0.262	275	0.198	5427	5702	100
3.017-3.164	0.254	251	0.191	5158	5409	100
3.164-3.334	0.242	243	0.186	5001	5245	99.981
3.334-3.535	0.245	244	0.178	4650	4894	100
3.535-3.778	0.255	249	0.172	4424	4678	99.893
3.778-4.078	0.228	245	0.148	4074	4324	99.884
4.078-4.464	0.178	213	0.142	3785	4011	99.676
4.464-4.985	0.187	199	0.138	3443	3659	99.535
4.985-5.745	0.18	168	0.169	3036	3234	99.072
5.745-7.008	0.227	154	0.191	2600	2791	98.674
7.008-9.796	0.171	115	0.149	2061	2209	98.506
9.796-45.596	0.251	61	0.202	1223	1348	95.252

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	1.7572	-0.0874	0.5008	2.7742	0.4648	3.1245	0.0699	0.2485	0.0374	-0.1273	-0.1134	0.2667	-0.1288	-0.2433	0.0435	-0.1754	-0.012	-0.0217	-0.0058	0.0445	-0.1502	73.8062	-48.0287	117.8956
2	2.9362	-0.4217	0.2397	1.154	-0.5012	3.0826	-0.0286	0.1334	-0.2224	-0.1023	0.0423	-0.1113	0.2848	0.2285	-0.0137	-0.1635	0.0449	0.0196	-0.1186	-0.0127	-0.1447	99.8015	-60.3083	135.7614
3	2.0096	-0.3193	0.0303	2.2696	0.4623	1.7967	-0.0429	-0.0879	0.343	0.107	0.0304	-0.0418	-0.208	0.0039	0.0125	-0.1112	-0.0163	0.0204	-0.1551	-0.0279	-0.0818	84.5443	-32.2089	146.4202
4	2.2743	0.272	-0.3376	3.1228	-0.8629	1.1433	0.0013	0.1809	0.0126	-0.0339	-0.004	0.301	-0.0966	-0.0221	0.0026	-0.0996	0.047	0.0225	-0.1739	-0.021	-0.1696	87.7967	16.5602	163.74
5	0.9246	-0.4146	0.3082	3.5322	-0.9727	2.4791	0.0243	-0.1156	-0.0294	0.5726	-0.0755	-0.1426	-0.2809	0.2388	0.0512	0.0195	-0.0112	0.0021	-0.0995	-0.018	-0.1913	101.4181	-1.3381	188.4967
6	2.6855	0.0524	0.6069	1.7772	-0.0317	1.9661	-0.0061	-0.0349	-0.4107	0.1161	0.0781	0.5836	0.0971	-0.1454	-0.072	-0.1186	-0.0031	0.0683	-0.1968	-0.0159	0.1741	73.6048	-13.1349	172.185
7	3.6883	-0.5514	-1.7128	1.5692	0.8635	3.5822	0.0801	0.3299	0.1728	-0.0253	-0.1267	0.3403	-0.2864	-0.4593	0.0466	-0.1057	0.0422	0.0107	-0.0922	-0.0128	-0.0408	28.7252	-32.8485	179.7907
8	4.0288	-1.8533	-0.535	3.6413	0.7417	1.3376	-0.4618	-0.3593	-0.2746	0.7661	0.3252	0.3165	0.5308	0.1105	0.1366	0.1676	0.057	0.099	-0.1297	0.0348	-0.1687	47.4716	-58.3863	190.7328
9	2.5065	-0.455	-0.6937	2.5919	-0.2145	3.234	0.1272	0.297	0.3041	-0.13	-0.0574	-0.2647	-0.0647	0.1667	-0.0698	-0.1749	-0.0351	0.0638	-0.1063	0.0044	-0.1169	57.1586	-40.9473	163.4089

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 - 230	1 - 230
2	2	B	B	1 - 230	1 - 230
3	3	C	C	1 - 238	1 - 238
4	4	D	D	1 - 229	1 - 229
5	5	E	E	1 - 236	1 - 236
6	6	F	F	1 - 226	1 - 226
7	7	G	G	1 - 230	1 - 230
8	8	H	H	1 - 231	1 - 231
9	9	I	I	1 - 229	1 - 229

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