PDB-4rmo: Crystal Structure of the CptIN Type III Toxin-Antitoxin System fr...

ID or keywords:

Entry

Database: PDB / ID: 4rmo

Title

Crystal Structure of the CptIN Type III Toxin-Antitoxin System from Eubacterium rectale

Components

CptN Toxin
RNA (45-MER)

Keywords

Toxin/RNA / protein-RNA complex / pseudoknot / RNA twist / toxin-antitoxin / type III / bacteriophage resistance / Toxin-RNA complex

Function / homology

Thiol Ester Dehydrase; Chain A - #130 / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta / RNA / RNA (> 10) / Uncharacterized protein

Function and homology information

Biological species

Eubacterium rectale DSM 17629 (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Rao, F. / Voss, J.E. / Short, F.L. / Luisi, B.F.

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system.
Authors: Rao, F. / Short, F.L. / Voss, J.E. / Blower, T.R. / Orme, A.L. / Whittaker, T.E. / Luisi, B.F. / Salmond, G.P.

History

Deposition	Oct 21, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references
Revision 1.2	Nov 18, 2015	Group: Database references
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rmo.cif.gz	504.9 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rm/4rmo ftp://data.pdbj.org/pub/pdb/validation_reports/rm/4rmo	HTTPS FTP

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Related structure data

Similar structure data	6cvp-d 3hym-8 4f0i-d 4rks-d 5ejv-d 1fq7-2 2gru-d 3sno-1 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: CptN Toxin

B: RNA (45-MER)

C: CptN Toxin

D: RNA (45-MER)

E: CptN Toxin

F: RNA (45-MER)

G: CptN Toxin

H: RNA (45-MER)

I: CptN Toxin

J: RNA (45-MER)

K: CptN Toxin

L: RNA (45-MER)

M: CptN Toxin

N: RNA (45-MER)

O: CptN Toxin

P: RNA (45-MER)

hetero molecules

268 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CptN Toxin

B: RNA (45-MER)

E: CptN Toxin

F: RNA (45-MER)

hetero molecules

defined by author&software
66.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: CptN Toxin

D: RNA (45-MER)

G: CptN Toxin

H: RNA (45-MER)

hetero molecules

defined by author&software
67.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: CptN Toxin

J: RNA (45-MER)

K: CptN Toxin

L: RNA (45-MER)

hetero molecules

defined by author&software
67 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: CptN Toxin

N: RNA (45-MER)

O: CptN Toxin

P: RNA (45-MER)

hetero molecules

defined by author&software
66.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.110, 185.891, 138.780
Angle α, β, γ (deg.)	90.00, 92.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	1	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
1	2	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	2	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
1	3	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	3	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
1	4	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	4	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
1	5	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	5	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
1	6	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	6	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	7	MSE	MSE	GLN	GLN	A	A	1 - 155	1 - 155
2	7	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	8	A	A	A23	A23	B	B	1 - 45	1 - 45
2	8	A	A	A23	A23	D	D	1 - 45	1 - 45
1	9	A	A	A23	A23	B	B	1 - 45	1 - 45
2	9	A	A	A23	A23	F	F	1 - 45	1 - 45
1	10	A	A	A23	A23	B	B	1 - 45	1 - 45
2	10	A	A	A23	A23	H	H	1 - 45	1 - 45
1	11	A	A	A23	A23	B	B	1 - 45	1 - 45
2	11	A	A	A23	A23	J	J	1 - 45	1 - 45
1	12	A	A	A23	A23	B	B	1 - 45	1 - 45
2	12	A	A	A23	A23	L	L	1 - 45	1 - 45
1	13	A	A	A23	A23	B	B	1 - 45	1 - 45
2	13	A	A	A23	A23	N	N	1 - 45	1 - 45
1	14	A	A	A23	A23	B	B	1 - 45	1 - 45
2	14	A	A	A23	A23	P	P	1 - 45	1 - 45
1	15	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	15	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
1	16	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	16	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
1	17	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	17	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
1	18	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	18	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
1	19	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	19	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	20	MSE	MSE	GLN	GLN	C	C	1 - 155	1 - 155
2	20	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	21	A	A	A23	A23	D	D	1 - 45	1 - 45
2	21	A	A	A23	A23	F	F	1 - 45	1 - 45
1	22	A	A	A23	A23	D	D	1 - 45	1 - 45
2	22	A	A	A23	A23	H	H	1 - 45	1 - 45
1	23	A	A	A23	A23	D	D	1 - 45	1 - 45
2	23	A	A	A23	A23	J	J	1 - 45	1 - 45
1	24	A	A	A23	A23	D	D	1 - 45	1 - 45
2	24	A	A	A23	A23	L	L	1 - 45	1 - 45
1	25	A	A	A23	A23	D	D	1 - 45	1 - 45
2	25	A	A	A23	A23	N	N	1 - 45	1 - 45
1	26	A	A	A23	A23	D	D	1 - 45	1 - 45
2	26	A	A	A23	A23	P	P	1 - 45	1 - 45
1	27	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
2	27	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
1	28	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
2	28	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
1	29	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
2	29	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
1	30	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
2	30	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	31	MSE	MSE	GLN	GLN	E	E	1 - 155	1 - 155
2	31	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	32	A	A	A23	A23	F	F	1 - 45	1 - 45
2	32	A	A	A23	A23	H	H	1 - 45	1 - 45
1	33	A	A	A23	A23	F	F	1 - 45	1 - 45
2	33	A	A	A23	A23	J	J	1 - 45	1 - 45
1	34	A	A	A23	A23	F	F	1 - 45	1 - 45
2	34	A	A	A23	A23	L	L	1 - 45	1 - 45
1	35	A	A	A23	A23	F	F	1 - 45	1 - 45
2	35	A	A	A23	A23	N	N	1 - 45	1 - 45
1	36	A	A	A23	A23	F	F	1 - 45	1 - 45
2	36	A	A	A23	A23	P	P	1 - 45	1 - 45
1	37	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
2	37	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
1	38	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
2	38	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
1	39	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
2	39	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	40	MSE	MSE	GLN	GLN	G	G	1 - 155	1 - 155
2	40	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	41	A	A	A23	A23	H	H	1 - 45	1 - 45
2	41	A	A	A23	A23	J	J	1 - 45	1 - 45
1	42	A	A	A23	A23	H	H	1 - 45	1 - 45
2	42	A	A	A23	A23	L	L	1 - 45	1 - 45
1	43	A	A	A23	A23	H	H	1 - 45	1 - 45
2	43	A	A	A23	A23	N	N	1 - 45	1 - 45
1	44	A	A	A23	A23	H	H	1 - 45	1 - 45
2	44	A	A	A23	A23	P	P	1 - 45	1 - 45
1	45	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
2	45	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
1	46	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
2	46	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	47	MSE	MSE	GLN	GLN	I	I	1 - 155	1 - 155
2	47	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	48	A	A	A23	A23	J	J	1 - 45	1 - 45
2	48	A	A	A23	A23	L	L	1 - 45	1 - 45
1	49	A	A	A23	A23	J	J	1 - 45	1 - 45
2	49	A	A	A23	A23	N	N	1 - 45	1 - 45
1	50	A	A	A23	A23	J	J	1 - 45	1 - 45
2	50	A	A	A23	A23	P	P	1 - 45	1 - 45
1	51	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
2	51	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
1	52	MSE	MSE	GLN	GLN	K	K	1 - 155	1 - 155
2	52	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	53	A	A	A23	A23	L	L	1 - 45	1 - 45
2	53	A	A	A23	A23	N	N	1 - 45	1 - 45
1	54	A	A	A23	A23	L	L	1 - 45	1 - 45
2	54	A	A	A23	A23	P	P	1 - 45	1 - 45
1	55	MSE	MSE	GLN	GLN	M	M	1 - 155	1 - 155
2	55	MSE	MSE	GLN	GLN	O	O	1 - 155	1 - 155
1	56	A	A	A23	A23	N	N	1 - 45	1 - 45
2	56	A	A	A23	A23	P	P	1 - 45	1 - 45

NCS ensembles :

#1: Protein	CptN Toxin Mass: 18696.795 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria) Strain: DSM 17629 / Gene: cptN, EUR_02830 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: D6E269
#2: RNA chain	RNA (45-MER) Mass: 14556.560 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	... ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.06	59.76
2

Crystal grow

Temperature: 293 K / Method: vapor diffusion / pH: 4.8
Details: CaCl2, 2-Propanol, Sodium Acetate, pH 4.8, vapor diffusion, temperature 293K

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Diamond	I02	1	0.9795
SYNCHROTRON	Diamond	I02	2	0.9795

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	May 8, 2013
DECTRIS PILATUS 6M	2	PIXEL	May 8, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Redundancy: 13.5 % / Number: 869571 / R_merge(I) obs: 0.164 / D res high: 3 Å / D res low: 93.27 Å / Num. obs: 64337 / % possible obs: 100 / Rejects: 580

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Redundancy
3	3.07	1	0.612	12.6
13.75	93.27	1	0.054	13.1

Reflection

Resolution: 2.2→63.12 Å / Num. obs: 157960 / % possible obs: 97.9 % / Redundancy: 2.3 % / R_merge(I) obs: 0.048 / Net I/σ(I): 11.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.2-2.24	2.1	0.338	2.4	1,2	97
12.05-63.04	2.6	0.022	37.4	1,2	96.9

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
Aimless	0.1.29	data scaling
SOLVE		phasing
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.15	data extraction
GDA		data collection
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→63.12 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.938 / SU B: 5.894 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2338 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23386	7919	5 %	RANDOM
R_work	0.19944	-	-	-
obs	0.2012	150001	97.85 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 40.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.65 Å²	0 Å²	0.57 Å²
2-	-	-0.23 Å²	0 Å²
3-	-	-	2.84 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→63.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10363	7696	48	1322	19429

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.016	19265
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	13810
X-RAY DIFFRACTION	r_angle_refined_deg	1.72	1.653	27710
X-RAY DIFFRACTION	r_angle_other_deg	1.854	3	32321
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.108	5	1248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.265	23.395	542
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.686	15	2040
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.687	15	87
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	2903
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	16037
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	4378
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9919	0.09
1	2	C	9919	0.09
2	1	A	9924	0.09
2	2	E	9924	0.09
3	1	A	9880	0.09
3	2	G	9880	0.09
4	1	A	9781	0.08
4	2	I	9781	0.08
5	1	A	9902	0.1
5	2	K	9902	0.1
6	1	A	9886	0.08
6	2	M	9886	0.08
7	1	A	9834	0.1
7	2	O	9834	0.1
8	1	B	3872	0.06
8	2	D	3872	0.06
9	1	B	3879	0.06
9	2	F	3879	0.06
10	1	B	3878	0.05
10	2	H	3878	0.05
11	1	B	3786	0.09
11	2	J	3786	0.09
12	1	B	3866	0.05
12	2	L	3866	0.05
13	1	B	3837	0.08
13	2	N	3837	0.08
14	1	B	3750	0.12
14	2	P	3750	0.12
15	1	C	9905	0.09
15	2	E	9905	0.09
16	1	C	9752	0.1
16	2	G	9752	0.1
17	1	C	9812	0.08
17	2	I	9812	0.08
18	1	C	9850	0.1
18	2	K	9850	0.1
19	1	C	9871	0.09
19	2	M	9871	0.09
20	1	C	9856	0.09
20	2	O	9856	0.09
21	1	D	3872	0.04
21	2	F	3872	0.04
22	1	D	3877	0.03
22	2	H	3877	0.03
23	1	D	3801	0.07
23	2	J	3801	0.07
24	1	D	3855	0.04
24	2	L	3855	0.04
25	1	D	3818	0.09
25	2	N	3818	0.09
26	1	D	3746	0.11
26	2	P	3746	0.11
27	1	E	9719	0.1
27	2	G	9719	0.1
28	1	E	9729	0.09
28	2	I	9729	0.09
29	1	E	9811	0.1
29	2	K	9811	0.1
30	1	E	9839	0.09
30	2	M	9839	0.09
31	1	E	9821	0.1
31	2	O	9821	0.1
32	1	F	3878	0.03
32	2	H	3878	0.03
33	1	F	3772	0.08
33	2	J	3772	0.08
34	1	F	3876	0.03
34	2	L	3876	0.03
35	1	F	3820	0.09
35	2	N	3820	0.09
36	1	F	3754	0.11
36	2	P	3754	0.11
37	1	G	9678	0.09
37	2	I	9678	0.09
38	1	G	9845	0.1
38	2	K	9845	0.1
39	1	G	9827	0.09
39	2	M	9827	0.09
40	1	G	9743	0.1
40	2	O	9743	0.1
41	1	H	3774	0.08
41	2	J	3774	0.08
42	1	H	3862	0.03
42	2	L	3862	0.03
43	1	H	3832	0.08
43	2	N	3832	0.08
44	1	H	3765	0.11
44	2	P	3765	0.11
45	1	I	9694	0.1
45	2	K	9694	0.1
46	1	I	9835	0.08
46	2	M	9835	0.08
47	1	I	9678	0.09
47	2	O	9678	0.09
48	1	J	3769	0.08
48	2	L	3769	0.08
49	1	J	3766	0.1
49	2	N	3766	0.1
50	1	J	3690	0.13
50	2	P	3690	0.13
51	1	K	9779	0.1
51	2	M	9779	0.1
52	1	K	9730	0.11
52	2	O	9730	0.11
53	1	L	3809	0.09
53	2	N	3809	0.09
54	1	L	3741	0.11
54	2	P	3741	0.11
55	1	M	9813	0.09
55	2	O	9813	0.09
56	1	N	3734	0.13
56	2	P	3734	0.13

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	556	-
R_work	0.305	11102	-
obs	-	-	97.19 %

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