PDB-2v5h: Controlling the storage of nitrogen as arginine: the complex of P...

ID or keywords:

Entry

Database: PDB / ID: 2v5h

Title

Controlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC 7942

Components

ACETYLGLUTAMATE KINASE
NITROGEN REGULATORY PROTEIN P-II

Keywords

TRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / TRANSFERASE / CYANOBACTERIA / N-ACETYL-L-GLUTAMATE KINASE / PII SIGNAL PROTEIN / NUCLEOTIDE-BINDING / ACETYLGLUTAMATE / PHOSPHORYLATION / AMINO ACID KINASE / GLNB / KINASE / TRIMER / HEXAMER / ATP-BINDING / ARGININE INHIBITION / ARGININE BIOSYNTHESIS

Function / homology

Function and homology information

acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process via ornithine / regulation of nitrogen utilization / L-arginine biosynthetic process / enzyme regulator activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function

Biological species

SYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Llacer, J.L. / Marco-Marin, C. / Gil-Ortiz, F. / Fita, I. / Rubio, V.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The Crystal Structure of the Complex of Pii and Acetylglutamate Kinase Reveals How Pii Controls the Storage of Nitrogen as Arginine.
Authors: Llacer, J.L. / Contreras, A. / Forchhammer, K. / Marco-Marin, C. / Gil-Ortiz, F. / Maldonado, R. / Fita, I. / Rubio, V.

History

Deposition	Jul 4, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 16, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 10, 2014	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2v5h.cif.gz	447.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2v5h_validation.pdf.gz	539.1 KB	Display	wwPDB validaton report
Full document	2v5h_full_validation.pdf.gz	584.7 KB	Display
Data in XML	2v5h_validation.xml.gz	82.9 KB	Display
Data in CIF	2v5h_validation.cif.gz	112.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5h ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5h	HTTPS FTP

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Related structure data

Related structure data	2jj4SC 1qy7 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2jj4-1 3134 2zi8-1 6vxn-d 1tf7-d 1z01-3 3x2r-d 1u9i-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: ACETYLGLUTAMATE KINASE

E: ACETYLGLUTAMATE KINASE

F: ACETYLGLUTAMATE KINASE

G: NITROGEN REGULATORY PROTEIN P-II

H: NITROGEN REGULATORY PROTEIN P-II

I: NITROGEN REGULATORY PROTEIN P-II

J: NITROGEN REGULATORY PROTEIN P-II

K: NITROGEN REGULATORY PROTEIN P-II

L: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

283 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	90.379, 161.027, 91.562
Angle α, β, γ (deg.)	90.00, 106.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	I	108 - 112
2	1	1	4	J	108 - 112
3	1	1	4	K	108 - 112
4	1	1	4	L	108 - 112
1	1	2	1	A	45
2	1	2	1	B	45
3	1	2	1	E	45
4	1	2	1	F	45
1	1	3	4	F	289 - 301
2	1	3	4	E	289 - 301
3	1	3	4	C	289 - 301
4	1	3	4	D	289 - 301
1	1	4	1	A	144
2	1	4	1	F	144
1	1	5	1	G	48 - 100
2	1	5	1	H	48 - 100
3	1	5	1	I	48 - 100
4	1	5	1	J	48 - 100
5	1	5	1	K	48 - 100
6	1	5	1	L	48 - 100
1	2	5	1	G	1 - 36
2	2	5	1	H	1 - 36
3	2	5	1	I	1 - 36
4	2	5	1	J	1 - 36
5	2	5	1	K	1 - 36
6	2	5	1	L	1 - 36
1	3	5	1	G	102 - 107
2	3	5	1	H	102 - 107
3	3	5	1	I	102 - 107
4	3	5	1	J	102 - 107
5	3	5	1	K	102 - 107
6	3	5	1	L	102 - 107
1	4	5	4	G	43 - 47
2	4	5	4	H	43 - 47
3	4	5	4	I	43 - 47
4	4	5	4	J	43 - 47
5	4	5	4	K	43 - 47
6	4	5	4	L	43 - 47
1	5	5	6	G	37 - 42
2	5	5	6	H	37 - 42
3	5	5	6	I	37 - 42
4	5	5	6	J	37 - 42
5	5	5	6	K	37 - 42
6	5	5	6	L	37 - 42
1	6	5	3	G	101
2	6	5	3	H	101
3	6	5	3	I	101
4	6	5	3	J	101
5	6	5	3	K	101
6	6	5	3	L	101
1	1	6	4	B	144
2	1	6	4	C	144
3	1	6	4	D	144
4	1	6	4	E	144
1	1	7	1	A	16 - 44
2	1	7	1	B	16 - 44
3	1	7	1	C	16 - 44
4	1	7	1	D	16 - 44
5	1	7	1	E	16 - 44
6	1	7	1	F	16 - 44
1	2	7	1	A	46 - 72
2	2	7	1	B	46 - 72
3	2	7	1	C	46 - 72
4	2	7	1	D	46 - 72
5	2	7	1	E	46 - 72
6	2	7	1	F	46 - 72
1	3	7	1	A	74 - 83
2	3	7	1	B	74 - 83
3	3	7	1	C	74 - 83
4	3	7	1	D	74 - 83
5	3	7	1	E	74 - 83
6	3	7	1	F	74 - 83
1	4	7	3	A	84
2	4	7	3	B	84
3	4	7	3	C	84
4	4	7	3	D	84
5	4	7	3	E	84
6	4	7	3	F	84
1	5	7	1	A	85 - 87
2	5	7	1	B	85 - 87
3	5	7	1	C	85 - 87
4	5	7	1	D	85 - 87
5	5	7	1	E	85 - 87
6	5	7	1	F	85 - 87
1	6	7	4	A	89
2	6	7	4	B	89
3	6	7	4	C	89
4	6	7	4	D	89
5	6	7	4	E	89
6	6	7	4	F	89
1	7	7	1	A	90
2	7	7	1	B	90
3	7	7	1	C	90
4	7	7	1	D	90
5	7	7	1	E	90
6	7	7	1	F	90
1	8	7	2	A	91
2	8	7	2	B	91
3	8	7	2	C	91
4	8	7	2	D	91
5	8	7	2	E	91
6	8	7	2	F	91
1	9	7	1	A	92 - 93
2	9	7	1	B	92 - 93
3	9	7	1	C	92 - 93
4	9	7	1	D	92 - 93
5	9	7	1	E	92 - 93
6	9	7	1	F	92 - 93
1	10	7	1	A	95 - 98
2	10	7	1	B	95 - 98
3	10	7	1	C	95 - 98
4	10	7	1	D	95 - 98
5	10	7	1	E	95 - 98
6	10	7	1	F	95 - 98
1	11	7	1	A	100 - 143
2	11	7	1	B	100 - 143
3	11	7	1	C	100 - 143
4	11	7	1	D	100 - 143
5	11	7	1	E	100 - 143
6	11	7	1	F	100 - 143
1	12	7	1	A	145 - 150
2	12	7	1	B	145 - 150
3	12	7	1	C	145 - 150
4	12	7	1	D	145 - 150
5	12	7	1	E	145 - 150
6	12	7	1	F	145 - 150
1	13	7	1	A	152 - 160
2	13	7	1	B	152 - 160
3	13	7	1	C	152 - 160
4	13	7	1	D	152 - 160
5	13	7	1	E	152 - 160
6	13	7	1	F	152 - 160
1	14	7	1	A	162 - 164
2	14	7	1	B	162 - 164
3	14	7	1	C	162 - 164
4	14	7	1	D	162 - 164
5	14	7	1	E	162 - 164
6	14	7	1	F	162 - 164
1	15	7	2	A	165 - 166
2	15	7	2	B	165 - 166
3	15	7	2	C	165 - 166
4	15	7	2	D	165 - 166
5	15	7	2	E	165 - 166
6	15	7	2	F	165 - 166
1	16	7	1	A	167 - 178
2	16	7	1	B	167 - 178
3	16	7	1	C	167 - 178
4	16	7	1	D	167 - 178
5	16	7	1	E	167 - 178
6	16	7	1	F	167 - 178
1	17	7	2	A	179
2	17	7	2	B	179
3	17	7	2	C	179
4	17	7	2	D	179
5	17	7	2	E	179
6	17	7	2	F	179
1	18	7	1	A	180 - 207
2	18	7	1	B	180 - 207
3	18	7	1	C	180 - 207
4	18	7	1	D	180 - 207
5	18	7	1	E	180 - 207
6	18	7	1	F	180 - 207
1	19	7	1	A	209 - 210
2	19	7	1	B	209 - 210
3	19	7	1	C	209 - 210
4	19	7	1	D	209 - 210
5	19	7	1	E	209 - 210
6	19	7	1	F	209 - 210
1	20	7	3	A	211
2	20	7	3	B	211
3	20	7	3	C	211
4	20	7	3	D	211
5	20	7	3	E	211
6	20	7	3	F	211
1	21	7	1	A	212 - 214
2	21	7	1	B	212 - 214
3	21	7	1	C	212 - 214
4	21	7	1	D	212 - 214
5	21	7	1	E	212 - 214
6	21	7	1	F	212 - 214
1	22	7	4	A	215 - 223
2	22	7	4	B	215 - 223
3	22	7	4	C	215 - 223
4	22	7	4	D	215 - 223
5	22	7	4	E	215 - 223
6	22	7	4	F	215 - 223
1	23	7	1	A	224 - 233
2	23	7	1	B	224 - 233
3	23	7	1	C	224 - 233
4	23	7	1	D	224 - 233
5	23	7	1	E	224 - 233
6	23	7	1	F	224 - 233
1	24	7	3	A	234
2	24	7	3	B	234
3	24	7	3	C	234
4	24	7	3	D	234
5	24	7	3	E	234
6	24	7	3	F	234
1	25	7	1	A	235 - 253
2	25	7	1	B	235 - 253
3	25	7	1	C	235 - 253
4	25	7	1	D	235 - 253
5	25	7	1	E	235 - 253
6	25	7	1	F	235 - 253
1	26	7	1	A	262 - 289
2	26	7	1	B	262 - 289
3	26	7	1	C	262 - 289
4	26	7	1	D	262 - 289
5	26	7	1	E	262 - 289
6	26	7	1	F	262 - 289
1	27	7	3	A	73
2	27	7	3	B	73
3	27	7	3	C	73
4	27	7	3	D	73
5	27	7	3	E	73
6	27	7	3	F	73
1	28	7	2	A	254
2	28	7	2	B	254
3	28	7	2	C	254
4	28	7	2	D	254
5	28	7	2	E	254
6	28	7	2	F	254
1	29	7	1	A	255 - 260
2	29	7	1	B	255 - 260
3	29	7	1	C	255 - 260
4	29	7	1	D	255 - 260
5	29	7	1	E	255 - 260
6	29	7	1	F	255 - 260
1	30	7	6	A	10 - 13
2	30	7	6	B	10 - 13
3	30	7	6	C	10 - 13
4	30	7	6	D	10 - 13
5	30	7	6	E	10 - 13
6	30	7	6	F	10 - 13
1	1	8	1	A	208
2	1	8	1	B	208
3	1	8	1	C	208
4	1	8	1	D	208
5	1	8	1	F	208
1	1	9	2	B	88
2	1	9	2	C	88
3	1	9	2	D	88
4	1	9	2	E	88
5	1	9	2	F	88
1	2	9	1	B	99
2	2	9	1	C	99
3	2	9	1	D	99
4	2	9	1	E	99
5	2	9	1	F	99
1	3	9	1	B	261
2	3	9	1	C	261
3	3	9	1	D	261
4	3	9	1	E	261
5	3	9	1	F	261
1	4	9	1	B	151
2	4	9	1	C	151
3	4	9	1	D	151
4	4	9	1	E	151
5	4	9	1	F	151
1	1	10	1	A	94
2	1	10	1	B	94
3	1	10	1	C	94
4	1	10	1	E	94
5	1	10	1	F	94
1	1	11	1	A	161
2	1	11	1	C	161
3	1	11	1	D	161
4	1	11	1	E	161
5	1	11	1	F	161

NCS ensembles :

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

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.399, 0.379, 0.835), (0.405, -0.744, 0.531), (0.823, 0.55, 0.143)	0.45982, -21.56274, 9.85157
2	given	(-0.804, -0.506, -0.311), (-0.496, 0.283, 0.821), (-0.327, 0.815, -0.479)	38.84369, -14.56789, 46.34348
3	given	(0.479, -0.766, 0.429), (-0.769, -0.601, -0.216), (0.423, -0.226, -0.877)	-3.14198, 18.71328, 44.80878
4	given	(-0.131, 0.99, 0.045), (-0.11, 0.031, -0.993), (-0.985, -0.135, 0.105)	17.94614, 29.15375, 41.2959
5	given	(-0.126, -0.117, -0.985), (0.99, 0.046, -0.132), (0.061, -0.992, 0.11)	46.23878, -13.10571, 23.56084
6	given	(0.47079, -0.76529, 0.43897), (-0.76721, -0.60079, -0.22459), (0.43561, -0.23104, -0.86998)	-3.66628, 19.25593, 44.10998

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Protein , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein	ACETYLGLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE Mass: 34492.391 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V1L5, acetylglutamate kinase
#2: Protein	NITROGEN REGULATORY PROTEIN P-II / PII PROTEIN / PII SIGNAL TRANSDUCING PROTEIN Mass: 12409.347 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3F4

#1: Protein

ACETYLGLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE

Mass: 34492.391 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-15B / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V1L5, acetylglutamate kinase

#2: Protein

NITROGEN REGULATORY PROTEIN P-II / PII PROTEIN / PII SIGNAL TRANSDUCING PROTEIN

Mass: 12409.347 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-22B / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3F4

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Non-polymers , 5 types, 206 molecules

#3: Chemical	ChemComp-NLG / N-ACETYL-L-GLUTAMATE Mass: 189.166 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₁₁NO₅
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	CATALYTIC ACTIVITY: ATP + N-ACETYL-L-GLUTAMATE = ADP + N-ACETYL-L- GLUTAMATE 5-PHOSPHATE P-II ...CATALYTIC ACTIVITY: ATP + N-ACETYL-L-GLUTAMATE = ADP + N-ACETYL-L- GLUTAMATE 5-PHOSPHATE P-II INDIRECTLY CONTROLS THE TRANSCRIPTION OF THE GS GENE (GLNA)
Sequence details	N-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH) CORRESPONDING TO A PET15B ...N-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH) CORRESPONDING TO A PET15B N-TERMINAL EXTRA HIS-TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 45.1 % / Description: NONE
Crystal grow	pH: 8.5 Details: 0.1 M TRIS-HCL PH 8.5, 0.15 M SODIUM ACETATE, 20% (WT/VOL) POLYETHYLENE GLYCOL 4K, 20 MM ACETYLGLUTAMATE.

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	ESRF	ID14-3	1	0.978
SYNCHROTRON	ESRF	BM16	2

Detector

Type	ID	Detector	Date	Details
ADSC CCD	1	CCD	Mar 21, 2006	RD COATED FLAT MIRROR AND RD COATED TOROIDAL MIRROR
MARRESEARCH	2	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SI111	SINGLE WAVELENGTH	M	x-ray	1
2			M	x-ray	1

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 2.75→87.71 Å / Num. obs: 65178 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / B_iso Wilson estimate: 61.3 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 6.9

Reflection shell

Resolution: 2.75→2.9 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJ4

2jj4

Resolution: 2.75→50 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.905 / SU B: 28.08 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	3297	5.1 %	RANDOM
R_work	0.2	-	-	-
obs	0.202	61827	100 %	-

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: 38.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	0.09 Å²
2-	-	-0.25 Å²	0 Å²
3-	-	-	0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17828	0	96	187	18111

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	18204
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.375	1.977	24614
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.396	5	2374
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.972	23.864	766
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.875	15	3194
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.311	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	2898
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	13594
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	8370
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	12505
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	675
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.237	0.2	52
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.389	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.394	1.5	11749
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.796	2	18917
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.419	3	6516
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.573	4.5	5697
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
2	1	A	9	tight positional	0.03	0.05
2	2	B	9	tight positional	0.03	0.05
2	3	E	9	tight positional	0.04	0.05
2	4	F	9	tight positional	0.03	0.05
4	1	A	9	tight positional	0.04	0.05
4	2	F	9	tight positional	0.04	0.05
5	1	G	724	tight positional	0.03	0.05
5	2	H	724	tight positional	0.03	0.05
5	3	I	724	tight positional	0.03	0.05
5	4	J	724	tight positional	0.04	0.05
5	5	K	724	tight positional	0.05	0.05
5	6	L	724	tight positional	0.04	0.05
7	1	A	1826	tight positional	0.04	0.05
7	2	B	1826	tight positional	0.04	0.05
7	3	C	1826	tight positional	0.03	0.05
7	4	D	1826	tight positional	0.03	0.05
7	5	E	1826	tight positional	0.04	0.05
7	6	F	1826	tight positional	0.03	0.05
8	1	A	7	tight positional	0.03	0.05
8	2	B	7	tight positional	0.02	0.05
8	3	C	7	tight positional	0.02	0.05
8	4	D	7	tight positional	0.03	0.05
8	5	F	7	tight positional	0.02	0.05
9	1	B	32	tight positional	0.04	0.05
9	2	C	32	tight positional	0.03	0.05
9	3	D	32	tight positional	0.03	0.05
9	4	E	32	tight positional	0.04	0.05
9	5	F	32	tight positional	0.02	0.05
10	1	A	7	tight positional	0.02	0.05
10	2	B	7	tight positional	0.02	0.05
10	3	C	7	tight positional	0.02	0.05
10	4	E	7	tight positional	0.01	0.05
10	5	F	7	tight positional	0.02	0.05
11	1	A	9	tight positional	0.15	0.05
11	2	C	9	tight positional	0.15	0.05
11	3	D	9	tight positional	0.14	0.05
11	4	E	9	tight positional	0.21	0.05
11	5	F	9	tight positional	0.21	0.05
1	1	I	8	medium positional	0.29	0.5
1	2	J	8	medium positional	0.29	0.5
1	3	K	8	medium positional	0.44	0.5
1	4	L	8	medium positional	0.26	0.5
3	1	F	17	medium positional	0.24	0.5
3	2	E	17	medium positional	0.29	0.5
3	3	C	17	medium positional	0.32	0.5
3	4	D	17	medium positional	0.45	0.5
5	1	G	50	medium positional	0.51	0.5
5	2	H	50	medium positional	0.29	0.5
5	3	I	50	medium positional	0.52	0.5
5	4	J	50	medium positional	0.53	0.5
5	5	K	50	medium positional	0.46	0.5
5	6	L	50	medium positional	0.41	0.5
6	1	B	9	medium positional	0.27	0.5
6	2	C	9	medium positional	0.61	0.5
6	3	D	9	medium positional	0.84	0.5
6	4	E	9	medium positional	0.28	0.5
7	1	A	87	medium positional	0.94	0.5
7	2	B	87	medium positional	0.82	0.5
7	3	C	87	medium positional	0.59	0.5
7	4	D	87	medium positional	0.63	0.5
7	5	E	87	medium positional	0.54	0.5
7	6	F	87	medium positional	0.58	0.5
9	1	B	6	medium positional	0.41	0.5
9	2	C	6	medium positional	0.44	0.5
9	3	D	6	medium positional	0.57	0.5
9	4	E	6	medium positional	0.21	0.5
9	5	F	6	medium positional	0.23	0.5
5	1	G	11	loose positional	0.8	5
5	2	H	11	loose positional	1.36	5
5	3	I	11	loose positional	0.74	5
5	4	J	11	loose positional	0.72	5
5	5	K	11	loose positional	0.76	5
5	6	L	11	loose positional	1.11	5
7	1	A	36	loose positional	1.56	5
7	2	B	36	loose positional	2.5	5
7	3	C	36	loose positional	1.11	5
7	4	D	36	loose positional	1.13	5
7	5	E	36	loose positional	1.28	5
7	6	F	36	loose positional	1.15	5
2	1	A	9	tight thermal	0.03	0.5
2	2	B	9	tight thermal	0.07	0.5
2	3	E	9	tight thermal	0.04	0.5
2	4	F	9	tight thermal	0.06	0.5
4	1	A	9	tight thermal	0.05	0.5
4	2	F	9	tight thermal	0.05	0.5
5	1	G	724	tight thermal	0.06	0.5
5	2	H	724	tight thermal	0.06	0.5
5	3	I	724	tight thermal	0.05	0.5
5	4	J	724	tight thermal	0.06	0.5
5	5	K	724	tight thermal	0.07	0.5
5	6	L	724	tight thermal	0.07	0.5
7	1	A	1826	tight thermal	0.08	0.5
7	2	B	1826	tight thermal	0.07	0.5
7	3	C	1826	tight thermal	0.07	0.5
7	4	D	1826	tight thermal	0.07	0.5
7	5	E	1826	tight thermal	0.07	0.5
7	6	F	1826	tight thermal	0.06	0.5
8	1	A	7	tight thermal	0.13	0.5
8	2	B	7	tight thermal	0.08	0.5
8	3	C	7	tight thermal	0.05	0.5
8	4	D	7	tight thermal	0.07	0.5
8	5	F	7	tight thermal	0.06	0.5
9	1	B	32	tight thermal	0.1	0.5
9	2	C	32	tight thermal	0.07	0.5
9	3	D	32	tight thermal	0.06	0.5
9	4	E	32	tight thermal	0.07	0.5
9	5	F	32	tight thermal	0.05	0.5
10	1	A	7	tight thermal	0.04	0.5
10	2	B	7	tight thermal	0.05	0.5
10	3	C	7	tight thermal	0.03	0.5
10	4	E	7	tight thermal	0.04	0.5
10	5	F	7	tight thermal	0.04	0.5
11	1	A	9	tight thermal	0.14	0.5
11	2	C	9	tight thermal	0.07	0.5
11	3	D	9	tight thermal	0.04	0.5
11	4	E	9	tight thermal	0.07	0.5
11	5	F	9	tight thermal	0.04	0.5
1	1	I	8	medium thermal	0.76	2
1	2	J	8	medium thermal	0.48	2
1	3	K	8	medium thermal	1.38	2
1	4	L	8	medium thermal	0.42	2
3	1	F	17	medium thermal	0.28	2
3	2	E	17	medium thermal	0.57	2
3	3	C	17	medium thermal	0.96	2
3	4	D	17	medium thermal	0.69	2
5	1	G	50	medium thermal	0.5	2
5	2	H	50	medium thermal	0.36	2
5	3	I	50	medium thermal	0.63	2
5	4	J	50	medium thermal	0.46	2
5	5	K	50	medium thermal	0.64	2
5	6	L	50	medium thermal	0.68	2
6	1	B	9	medium thermal	0.23	2
6	2	C	9	medium thermal	0.27	2
6	3	D	9	medium thermal	0.66	2
6	4	E	9	medium thermal	0.82	2
7	1	A	87	medium thermal	0.64	2
7	2	B	87	medium thermal	0.44	2
7	3	C	87	medium thermal	0.36	2
7	4	D	87	medium thermal	0.81	2
7	5	E	87	medium thermal	0.47	2
7	6	F	87	medium thermal	0.27	2
9	1	B	6	medium thermal	0.19	2
9	2	C	6	medium thermal	0.54	2
9	3	D	6	medium thermal	0.38	2
9	4	E	6	medium thermal	0.29	2
9	5	F	6	medium thermal	0.59	2
5	1	G	11	loose thermal	0.68	10
5	2	H	11	loose thermal	1.58	10
5	3	I	11	loose thermal	1.77	10
5	4	J	11	loose thermal	1.3	10
5	5	K	11	loose thermal	1	10
5	6	L	11	loose thermal	2.09	10
7	1	A	36	loose thermal	2.18	10
7	2	B	36	loose thermal	1.87	10
7	3	C	36	loose thermal	2.3	10
7	4	D	36	loose thermal	1.62	10
7	5	E	36	loose thermal	1.08	10
7	6	F	36	loose thermal	1.28	10

LS refinement shell

Resolution: 2.75→2.82 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.419	224	-
R_work	0.323	4563	-
obs	-	-	100 %

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	1.777	0.0796	-0.1732	2.3412	-0.8042	2.4885	0.1286	-0.153	0.1365	0.2655	-0.1672	-0.1267	-0.248	0.1404	0.0386	-0.1164	-0.0338	-0.0462	-0.2333	-0.0172	-0.1577	29.937	27.125	44.641
2	1.9065	0.2963	-0.3077	2.6621	0.7579	2.0123	-0.0028	-0.2061	-0.1286	0.1759	-0.0872	-0.178	0.2027	0.1631	0.09	-0.1266	-0.0002	-0.0518	-0.1878	0.0723	-0.1759	35.876	-6.35	55.922
3	2.3814	0.0826	0.4417	1.4672	-0.0811	3.0277	0.0307	0.0183	0.1569	0.0784	-0.1005	0.2298	-0.1178	-0.47	0.0699	-0.1914	0.0693	0.0061	0.0087	-0.0607	-0.1065	-12.819	14.99	37.36
4	3.0545	-0.179	-0.1492	1.7755	-0.1979	1.5135	-0.0847	0.2953	-0.3826	-0.0657	-0.0617	0.1653	0.2067	-0.1666	0.1465	-0.0625	-0.11	0.0525	-0.1274	-0.1851	0.0229	9.372	-30.25	12.166
5	1.883	0.6053	0.1627	2.7004	0.1612	2.9025	-0.1514	0.2195	-0.1899	-0.2071	0.0053	-0.2712	0.1262	0.2622	0.1461	-0.1407	0.012	0.0753	-0.1755	-0.003	-0.0977	42.682	-17.482	12.555
6	2.7844	-0.3623	-0.5354	2.0937	0.2815	2.0751	-0.1054	0.4518	0.0149	-0.2184	0.0143	0.1546	-0.0828	-0.4009	0.091	-0.1178	0.0688	-0.0778	0.1067	-0.003	-0.1828	-4.574	11.465	2.885
7	2.57	-1.474	0.2082	4.5892	-2.0014	1.823	-0.1114	-0.4066	-0.2021	0.4206	0.0298	0.262	0.0177	-0.4822	0.0817	-0.0304	-0.0416	0.0944	0.0134	-0.0616	0.0498	-6.919	-13.174	54.861
8	6.3014	2.8523	1.8801	2.1759	0.0284	1.3258	0.1214	-0.2129	-0.5823	0.3897	-0.0965	0.0525	0.2413	-0.3141	-0.025	-0.0078	-0.0315	0.0849	-0.0173	0.0529	-0.0204	8.544	-24.568	55.618
9	2.1929	-0.0177	-1.6366	2.8129	1.401	4.3429	-0.1153	0.0675	-0.5903	0.1324	-0.0783	0.2442	0.2279	-0.4188	0.1935	0.0668	-0.095	0.0586	0.0007	-0.0381	0.1325	-5.828	-27.387	42.367
10	5.7124	0.7485	0.0438	1.0703	-0.7976	1.5561	0.0739	0.5154	-0.005	-0.2521	-0.1012	-0.1521	-0.1612	-0.0367	0.0274	0.0402	0.0261	-0.0399	-0.0472	0.0537	-0.1253	27.17	20.09	-3.453
11	1.7463	-1.0202	-0.9601	5.2714	-0.4276	0.8885	-0.061	0.2833	0.08	-0.2388	0.0428	-0.4429	-0.0392	0.118	0.0181	-0.0782	0.0459	0.0318	-0.0373	0.0921	-0.1262	43.526	15	5.15
12	1.3932	0.8406	0.3194	1.9679	0.8711	5.5871	-0.047	0.2419	0.362	-0.2171	-0.0424	-0.0731	-0.3651	-0.0433	0.0895	-0.1551	0.037	0.0399	-0.1537	0.0547	-0.0523	33.716	30.529	11.681

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 291
2	X-RAY DIFFRACTION	1	A	1292
3	X-RAY DIFFRACTION	2	B	8 - 296
4	X-RAY DIFFRACTION	2	B	1297
5	X-RAY DIFFRACTION	3	C	8 - 291
6	X-RAY DIFFRACTION	3	C	1292
7	X-RAY DIFFRACTION	4	D	8 - 293
8	X-RAY DIFFRACTION	4	D	1294
9	X-RAY DIFFRACTION	5	E	8 - 293
10	X-RAY DIFFRACTION	5	E	1294
11	X-RAY DIFFRACTION	6	F	6 - 292
12	X-RAY DIFFRACTION	6	F	1293
13	X-RAY DIFFRACTION	7	G	1 - 111
14	X-RAY DIFFRACTION	8	H	1 - 108
15	X-RAY DIFFRACTION	9	I	1 - 111
16	X-RAY DIFFRACTION	10	J	1 - 110
17	X-RAY DIFFRACTION	11	K	1 - 108
18	X-RAY DIFFRACTION	12	L	1 - 109

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