PDB-8vwl: Crystal structure of Vibrio cholerae NFeoB in the apo form

ID or keywords:

Entry

Database: PDB / ID: 8vwl

Title

Crystal structure of Vibrio cholerae NFeoB in the apo form

Components

Ferrous iron transport protein B

Keywords

TRANSPORT PROTEIN / iron / transport / Feo / G-protein

Function / homology

Function and homology information

ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.67 Å

Authors

Lee, M. / Smith, A.T.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM133497	United States
National Science Foundation (NSF, United States)	CHE1844624	United States

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity.
Authors: Lee, M. / Magante, K. / Gomez-Garzon, C. / Payne, S.M. / Smith, A.T.

History

Deposition	Feb 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vwl.cif.gz	432.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8vwl.ent.gz	322.8 KB	Display	PDB format
PDBx/mmJSON format	8vwl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vwl_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8vwl_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8vwl_validation.xml.gz	72.6 KB	Display
Data in CIF	8vwl_validation.cif.gz	92.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/8vwl ftp://data.pdbj.org/pub/pdb/validation_reports/vw/8vwl	HTTPS FTP

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Related structure data

Related structure data	8vwnC 9ba6C 9ba7C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ferrous iron transport protein B

B: Ferrous iron transport protein B

C: Ferrous iron transport protein B

D: Ferrous iron transport protein B

E: Ferrous iron transport protein B

F: Ferrous iron transport protein B

G: Ferrous iron transport protein B

H: Ferrous iron transport protein B

hetero molecules

257 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ferrous iron transport protein B

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ferrous iron transport protein B

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Ferrous iron transport protein B

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Ferrous iron transport protein B

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Ferrous iron transport protein B

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Ferrous iron transport protein B

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Ferrous iron transport protein B

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Ferrous iron transport protein B

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.348, 84.118, 158.028
Angle α, β, γ (deg.)	76.170, 83.910, 74.510
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 4 through 24 or resid 41...
d_2	ens_1	(chain "C" and (resid 4 through 24 or resid 41...
d_3	ens_1	(chain "D" and (resid 4 through 24 or resid 41...
d_4	ens_1	(chain "E" and (resid 4 through 24 or resid 41...
d_5	ens_1	(chain "F" and (resid 4 through 24 or resid 41...
d_6	ens_1	(chain "G" and (resid 4 through 24 or resid 41...
d_7	ens_1	(chain "H" and (resid 4 through 24 or resid 41...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	GLN	GLN	GLY	GLY	A	A	4 - 24	4 - 24
d_1	2	THR	THR	THR	THR	A	A	41	41
d_1	3	PHE	PHE	ASP	ASP	A	A	44 - 49	44 - 49
d_1	4	PHE	PHE	ALA	ALA	A	A	51 - 61	51 - 61
d_1	5	ILE	ILE	SER	SER	A	A	71 - 77	71 - 77
d_1	6	ALA	ALA	THR	THR	A	A	79 - 82	79 - 82
d_1	7	PRO	PRO	LEU	LEU	A	A	84 - 110	84 - 110
d_1	8	ARG	ARG	LEU	LEU	A	A	112 - 124	112 - 124
d_1	9	ARG	ARG	ARG	ARG	A	A	126	126
d_1	10	LEU	LEU	LEU	LEU	A	A	131 - 133	131 - 133
d_1	11	GLN	GLN	LEU	LEU	A	A	135 - 145	135 - 145
d_1	12	ASN	ASN	ASN	ASN	A	A	151	151
d_1	13	GLN	GLN	VAL	VAL	A	A	154 - 155	154 - 155
d_1	14	PHE	PHE	LYS	LYS	A	A	158 - 159	158 - 159
d_1	15	LYS	LYS	HIS	HIS	A	A	161 - 163	161 - 163
d_1	16	LEU	LEU	GLN	GLN	A	A	165 - 168	165 - 168
d_1	17	ALA	ALA	LEU	LEU	A	A	171 - 172	171 - 172
d_1	18	LEU	LEU	ALA	ALA	A	A	177 - 181	177 - 181
d_1	19	PHE	PHE	ALA	ALA	A	A	183 - 195	183 - 195
d_1	20	GLN	GLN	ASP	ASP	A	A	197 - 212	197 - 212
d_1	21	LEU	LEU	ILE	ILE	A	A	214 - 216	214 - 216
d_1	22	GLY	GLY	LYS	LYS	A	A	218 - 220	218 - 220
d_1	23	ALA	ALA	GLU	GLU	A	A	222 - 223	222 - 223
d_1	24	GLN	GLN	VAL	VAL	A	A	225 - 227	225 - 227
d_1	25	GLN	GLN	HIS	HIS	A	A	229 - 232	229 - 232
d_1	26	CYS	CYS	HIS	HIS	A	A	234 - 251	234 - 251
d_1	27	LEU	LEU	VAL	VAL	A	A	253 - 257	253 - 257
d_2	1	GLN	GLN	GLY	GLY	C	C	4 - 24	4 - 24
d_2	2	THR	THR	THR	THR	C	C	41	41
d_2	3	PHE	PHE	ASP	ASP	C	C	44 - 49	44 - 49
d_2	4	PHE	PHE	ALA	ALA	C	C	51 - 61	51 - 61
d_2	5	ILE	ILE	SER	SER	C	C	71 - 77	71 - 77
d_2	6	ALA	ALA	THR	THR	C	C	79 - 82	79 - 82
d_2	7	PRO	PRO	LEU	LEU	C	C	84 - 110	84 - 110
d_2	8	ARG	ARG	LEU	LEU	C	C	112 - 124	112 - 124
d_2	9	ARG	ARG	ARG	ARG	C	C	126	126
d_2	10	LEU	LEU	LEU	LEU	C	C	131 - 133	131 - 133
d_2	11	GLN	GLN	LEU	LEU	C	C	135 - 145	135 - 145
d_2	12	ASN	ASN	ASN	ASN	C	C	151	151
d_2	13	GLN	GLN	VAL	VAL	C	C	154 - 155	154 - 155
d_2	14	PHE	PHE	LYS	LYS	C	C	158 - 159	158 - 159
d_2	15	LYS	LYS	HIS	HIS	C	C	161 - 163	161 - 163
d_2	16	LEU	LEU	GLN	GLN	C	C	165 - 168	165 - 168
d_2	17	ALA	ALA	LEU	LEU	C	C	171 - 172	171 - 172
d_2	18	LEU	LEU	ALA	ALA	C	C	177 - 181	177 - 181
d_2	19	PHE	PHE	ALA	ALA	C	C	183 - 195	183 - 195
d_2	20	GLN	GLN	ASP	ASP	C	C	197 - 212	197 - 212
d_2	21	LEU	LEU	ILE	ILE	C	C	214 - 216	214 - 216
d_2	22	GLY	GLY	LYS	LYS	C	C	218 - 220	218 - 220
d_2	23	ALA	ALA	GLU	GLU	C	C	222 - 223	222 - 223
d_2	24	GLN	GLN	VAL	VAL	C	C	225 - 227	225 - 227
d_2	25	GLN	GLN	HIS	HIS	C	C	229 - 232	229 - 232
d_2	26	CYS	CYS	HIS	HIS	C	C	234 - 251	234 - 251
d_2	27	LEU	LEU	VAL	VAL	C	C	253 - 257	253 - 257
d_3	1	GLN	GLN	GLY	GLY	D	D	4 - 24	4 - 24
d_3	2	THR	THR	THR	THR	D	D	41	41
d_3	3	PHE	PHE	ASP	ASP	D	D	44 - 49	44 - 49
d_3	4	PHE	PHE	ALA	ALA	D	D	51 - 61	51 - 61
d_3	5	ILE	ILE	SER	SER	D	D	71 - 77	71 - 77
d_3	6	ALA	ALA	THR	THR	D	D	79 - 82	79 - 82
d_3	7	PRO	PRO	LEU	LEU	D	D	84 - 110	84 - 110
d_3	8	ARG	ARG	LEU	LEU	D	D	112 - 124	112 - 124
d_3	9	ARG	ARG	ARG	ARG	D	D	126	126
d_3	10	LEU	LEU	LEU	LEU	D	D	131 - 133	131 - 133
d_3	11	GLN	GLN	LEU	LEU	D	D	135 - 145	135 - 145
d_3	12	ASN	ASN	ASN	ASN	D	D	151	151
d_3	13	GLN	GLN	VAL	VAL	D	D	154 - 155	154 - 155
d_3	14	PHE	PHE	LYS	LYS	D	D	158 - 159	158 - 159
d_3	15	LYS	LYS	HIS	HIS	D	D	161 - 163	161 - 163
d_3	16	LEU	LEU	GLN	GLN	D	D	165 - 168	165 - 168
d_3	17	ALA	ALA	LEU	LEU	D	D	171 - 172	171 - 172
d_3	18	LEU	LEU	ALA	ALA	D	D	177 - 181	177 - 181
d_3	19	PHE	PHE	ALA	ALA	D	D	183 - 195	183 - 195
d_3	20	GLN	GLN	ASP	ASP	D	D	197 - 212	197 - 212
d_3	21	LEU	LEU	ILE	ILE	D	D	214 - 216	214 - 216
d_3	22	GLY	GLY	LYS	LYS	D	D	218 - 220	218 - 220
d_3	23	ALA	ALA	GLU	GLU	D	D	222 - 223	222 - 223
d_3	24	GLN	GLN	VAL	VAL	D	D	225 - 227	225 - 227
d_3	25	GLN	GLN	HIS	HIS	D	D	229 - 232	229 - 232
d_3	26	CYS	CYS	HIS	HIS	D	D	234 - 251	234 - 251
d_3	27	LEU	LEU	VAL	VAL	D	D	253 - 257	253 - 257
d_4	1	GLN	GLN	GLY	GLY	E	E	4 - 24	4 - 24
d_4	2	THR	THR	THR	THR	E	E	41	41
d_4	3	PHE	PHE	ASP	ASP	E	E	44 - 49	44 - 49
d_4	4	PHE	PHE	ALA	ALA	E	E	51 - 61	51 - 61
d_4	5	ILE	ILE	SER	SER	E	E	71 - 77	71 - 77
d_4	6	ALA	ALA	THR	THR	E	E	79 - 82	79 - 82
d_4	7	PRO	PRO	LEU	LEU	E	E	84 - 110	84 - 110
d_4	8	ARG	ARG	LEU	LEU	E	E	112 - 124	112 - 124
d_4	9	ARG	ARG	ARG	ARG	E	E	126	126
d_4	10	LEU	LEU	LEU	LEU	E	E	131 - 133	131 - 133
d_4	11	GLN	GLN	LEU	LEU	E	E	135 - 145	135 - 145
d_4	12	ASN	ASN	ASN	ASN	E	E	151	151
d_4	13	GLN	GLN	VAL	VAL	E	E	154 - 155	154 - 155
d_4	14	PHE	PHE	LYS	LYS	E	E	158 - 159	158 - 159
d_4	15	LYS	LYS	HIS	HIS	E	E	161 - 163	161 - 163
d_4	16	LEU	LEU	GLN	GLN	E	E	165 - 168	165 - 168
d_4	17	ALA	ALA	LEU	LEU	E	E	171 - 172	171 - 172
d_4	18	LEU	LEU	ALA	ALA	E	E	177 - 181	177 - 181
d_4	19	PHE	PHE	ALA	ALA	E	E	183 - 195	183 - 195
d_4	20	GLN	GLN	ASP	ASP	E	E	197 - 212	197 - 212
d_4	21	LEU	LEU	ILE	ILE	E	E	214 - 216	214 - 216
d_4	22	GLY	GLY	LYS	LYS	E	E	218 - 220	218 - 220
d_4	23	ALA	ALA	GLU	GLU	E	E	222 - 223	222 - 223
d_4	24	GLN	GLN	VAL	VAL	E	E	225 - 227	225 - 227
d_4	25	GLN	GLN	HIS	HIS	E	E	229 - 232	229 - 232
d_4	26	CYS	CYS	HIS	HIS	E	E	234 - 251	234 - 251
d_4	27	LEU	LEU	VAL	VAL	E	E	253 - 257	253 - 257
d_5	1	GLN	GLN	GLY	GLY	F	F	4 - 24	4 - 24
d_5	2	THR	THR	THR	THR	F	F	41	41
d_5	3	PHE	PHE	ASP	ASP	F	F	44 - 49	44 - 49
d_5	4	PHE	PHE	ALA	ALA	F	F	51 - 61	51 - 61
d_5	5	ILE	ILE	SER	SER	F	F	71 - 77	71 - 77
d_5	6	ALA	ALA	THR	THR	F	F	79 - 82	79 - 82
d_5	7	PRO	PRO	LEU	LEU	F	F	84 - 110	84 - 110
d_5	8	ARG	ARG	LEU	LEU	F	F	112 - 124	112 - 124
d_5	9	ARG	ARG	ARG	ARG	F	F	126	126
d_5	10	LEU	LEU	LEU	LEU	F	F	131 - 133	131 - 133
d_5	11	GLN	GLN	LEU	LEU	F	F	135 - 145	135 - 145
d_5	12	ASN	ASN	ASN	ASN	F	F	151	151
d_5	13	GLN	GLN	VAL	VAL	F	F	154 - 155	154 - 155
d_5	14	PHE	PHE	LYS	LYS	F	F	158 - 159	158 - 159
d_5	15	LYS	LYS	HIS	HIS	F	F	161 - 163	161 - 163
d_5	16	LEU	LEU	GLN	GLN	F	F	165 - 168	165 - 168
d_5	17	ALA	ALA	LEU	LEU	F	F	171 - 172	171 - 172
d_5	18	LEU	LEU	ALA	ALA	F	F	177 - 181	177 - 181
d_5	19	PHE	PHE	ALA	ALA	F	F	183 - 195	183 - 195
d_5	20	GLN	GLN	ASP	ASP	F	F	197 - 212	197 - 212
d_5	21	LEU	LEU	ILE	ILE	F	F	214 - 216	214 - 216
d_5	22	GLY	GLY	LYS	LYS	F	F	218 - 220	218 - 220
d_5	23	ALA	ALA	GLU	GLU	F	F	222 - 223	222 - 223
d_5	24	GLN	GLN	VAL	VAL	F	F	225 - 227	225 - 227
d_5	25	GLN	GLN	HIS	HIS	F	F	229 - 232	229 - 232
d_5	26	CYS	CYS	HIS	HIS	F	F	234 - 251	234 - 251
d_5	27	LEU	LEU	VAL	VAL	F	F	253 - 257	253 - 257
d_6	1	GLN	GLN	GLY	GLY	G	G	4 - 24	4 - 24
d_6	2	THR	THR	THR	THR	G	G	41	41
d_6	3	PHE	PHE	ASP	ASP	G	G	44 - 49	44 - 49
d_6	4	PHE	PHE	ALA	ALA	G	G	51 - 61	51 - 61
d_6	5	ILE	ILE	SER	SER	G	G	71 - 77	71 - 77
d_6	6	ALA	ALA	THR	THR	G	G	79 - 82	79 - 82
d_6	7	PRO	PRO	LEU	LEU	G	G	84 - 110	84 - 110
d_6	8	ARG	ARG	LEU	LEU	G	G	112 - 124	112 - 124
d_6	9	ARG	ARG	ARG	ARG	G	G	126	126
d_6	10	LEU	LEU	LEU	LEU	G	G	131 - 133	131 - 133
d_6	11	GLN	GLN	LEU	LEU	G	G	135 - 145	135 - 145
d_6	12	ASN	ASN	ASN	ASN	G	G	151	151
d_6	13	GLN	GLN	VAL	VAL	G	G	154 - 155	154 - 155
d_6	14	PHE	PHE	LYS	LYS	G	G	158 - 159	158 - 159
d_6	15	LYS	LYS	HIS	HIS	G	G	161 - 163	161 - 163
d_6	16	LEU	LEU	GLN	GLN	G	G	165 - 168	165 - 168
d_6	17	ALA	ALA	LEU	LEU	G	G	171 - 172	171 - 172
d_6	18	LEU	LEU	ALA	ALA	G	G	177 - 181	177 - 181
d_6	19	PHE	PHE	ALA	ALA	G	G	183 - 195	183 - 195
d_6	20	GLN	GLN	ASP	ASP	G	G	197 - 212	197 - 212
d_6	21	LEU	LEU	ILE	ILE	G	G	214 - 216	214 - 216
d_6	22	GLY	GLY	LYS	LYS	G	G	218 - 220	218 - 220
d_6	23	ALA	ALA	GLU	GLU	G	G	222 - 223	222 - 223
d_6	24	GLN	GLN	VAL	VAL	G	G	225 - 227	225 - 227
d_6	25	GLN	GLN	HIS	HIS	G	G	229 - 232	229 - 232
d_6	26	CYS	CYS	HIS	HIS	G	G	234 - 251	234 - 251
d_6	27	LEU	LEU	VAL	VAL	G	G	253 - 257	253 - 257
d_7	1	GLN	GLN	GLY	GLY	H	H	4 - 24	4 - 24
d_7	2	THR	THR	ASP	ASP	H	H	41 - 49	41 - 49
d_7	3	PHE	PHE	ALA	ALA	H	H	51 - 61	51 - 61
d_7	4	ILE	ILE	SER	SER	H	H	71 - 77	71 - 77
d_7	5	ALA	ALA	THR	THR	H	H	79 - 82	79 - 82
d_7	6	PRO	PRO	LEU	LEU	H	H	84 - 110	84 - 110
d_7	7	ARG	ARG	LEU	LEU	H	H	112 - 124	112 - 124
d_7	8	ARG	ARG	ARG	ARG	H	H	126	126
d_7	9	LEU	LEU	LEU	LEU	H	H	131 - 133	131 - 133
d_7	10	GLN	GLN	LEU	LEU	H	H	135 - 145	135 - 145
d_7	11	ASN	ASN	ASN	ASN	H	H	151	151
d_7	12	GLN	GLN	VAL	VAL	H	H	154 - 155	154 - 155
d_7	13	PHE	PHE	LYS	LYS	H	H	158 - 159	158 - 159
d_7	14	LYS	LYS	HIS	HIS	H	H	161 - 163	161 - 163
d_7	15	LEU	LEU	GLN	GLN	H	H	165 - 168	165 - 168
d_7	16	ALA	ALA	LEU	LEU	H	H	171 - 172	171 - 172
d_7	17	LEU	LEU	ALA	ALA	H	H	177 - 181	177 - 181
d_7	18	PHE	PHE	ALA	ALA	H	H	183 - 195	183 - 195
d_7	19	GLN	GLN	ASP	ASP	H	H	197 - 212	197 - 212
d_7	20	LEU	LEU	ILE	ILE	H	H	214 - 216	214 - 216
d_7	21	GLY	GLY	LYS	LYS	H	H	218 - 220	218 - 220
d_7	22	ALA	ALA	GLU	GLU	H	H	222 - 223	222 - 223
d_7	23	GLN	GLN	VAL	VAL	H	H	225 - 227	225 - 227
d_7	24	GLN	GLN	HIS	HIS	H	H	229 - 232	229 - 232
d_7	25	CYS	CYS	HIS	HIS	H	H	234 - 251	234 - 251
d_7	26	LEU	LEU	VAL	VAL	H	H	253 - 257	253 - 257

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.998102027344, 0.0184123286385, -0.0587650335369), (0.0177568611355, -0.82767780116, -0.560922589444), (-0.0589664048005, -0.560901456247, 0.825779946163)	14.6078452407, 18.4277434359, -77.4090499439
2	given	(0.993408228756, 0.0948619275719, 0.0643529776833), (0.0172213781106, -0.678530922324, 0.734369941913), (0.113329233543, -0.728420896287, -0.675691854826)	8.64241638683, 40.7573886842, -104.192095539
3	given	(-0.989640370447, -0.0148235123463, 0.142801262823), (0.0654644792315, 0.838640663204, 0.540736756638), (-0.127774563749, 0.544483334457, -0.828982243089)	18.6368199816, 15.5196361111, -124.500700651
4	given	(-0.99072477164, -0.016242935174, 0.13490957681), (0.0474220724086, -0.971737000444, 0.231253862705), (0.127340386, 0.23550662204, 0.963494191507)	10.0185860383, 32.7800354449, -4.88902181965
5	given	(0.9916836968, 0.0116209937541, -0.128173312376), (0.0122575157243, -0.999916143629, 0.00417839905543), (-0.128114007078, -0.00571473661389, -0.991742982317)	-2.4905035406, 28.681519201, -37.7395446222
6	given	(0.991647596057, 0.0233993865735, -0.126836563904), (-0.109628180035, 0.670986375682, -0.73332049323), (0.0679463566144, 0.741100365913, 0.667947258596)	5.87234167028, -5.97183546905, -99.3781157697

#1: Protein	Ferrous iron transport protein B Mass: 32151.859 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: feoB_1, ERS013165_00117 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655NVH2
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M bis-tris pH 5.5

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Data collection

Diffraction	Mean temperature: 77 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.67→77.59 Å / Num. obs: 24215 / % possible obs: 95 % / Redundancy: 1.9 % / B_iso Wilson estimate: 131.98 Å² / CC_1/2: 0.998 / Net I/σ(I): 7
Reflection shell	Resolution: 3.67→3.73 Å / Num. unique obs: 1142 / CC_1/2: 0.792

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.67→77.57 Å / SU ML: 0.6642 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.3806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2698	1204	4.98 %
R_work	0.2086	22982	-
obs	0.2115	24186	94.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 147.06 Å²

Refinement step

Cycle: LAST / Resolution: 3.67→77.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15751	0	6	0	15757

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	15955
X-RAY DIFFRACTION	f_angle_d	0.6194	21531
X-RAY DIFFRACTION	f_chiral_restr	0.0409	2539
X-RAY DIFFRACTION	f_plane_restr	0.0045	2778
X-RAY DIFFRACTION	f_dihedral_angle_d	19.2442	6017

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.733516507082
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	0.797347082437
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.756528050072
ens_1	d_5	A	A	X-RAY DIFFRACTION	Torsion NCS	0.737577784947
ens_1	d_6	A	A	X-RAY DIFFRACTION	Torsion NCS	0.71400441924
ens_1	d_7	A	A	X-RAY DIFFRACTION	Torsion NCS	0.828515218363

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.67-3.82	0.4165	135	0.3589	2453	X-RAY DIFFRACTION	91.87
3.82-3.99	0.3753	130	0.3045	2517	X-RAY DIFFRACTION	92.98
3.99-4.2	0.3405	135	0.2859	2431	X-RAY DIFFRACTION	91.12
4.2-4.46	0.2918	142	0.2247	2512	X-RAY DIFFRACTION	92.6
4.46-4.81	0.2533	133	0.207	2632	X-RAY DIFFRACTION	98.19
4.81-5.29	0.2972	131	0.211	2660	X-RAY DIFFRACTION	98.31
5.29-6.06	0.2905	137	0.2379	2634	X-RAY DIFFRACTION	97.3
6.06-7.63	0.2879	136	0.2207	2571	X-RAY DIFFRACTION	96.4
7.63-77.57	0.1855	125	0.1343	2572	X-RAY DIFFRACTION	95.4

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