PDB-1yae: Structure of the Kainate Receptor Subunit GluR6 Agonist Binding D...

Basic information

• Entry: Database: PDB / ID: 1yae
• Title: Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with Domoic Acid
• Components: Glutamate receptor, ionotropic kainate 2
• Keywords: MEMBRANE PROTEIN / kainate receptor / glutamate receptor

Function / homology

Function:

mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / neuronal action potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / regulation of membrane potential / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / ubiquitin protein ligase binding / membrane / identical protein binding / plasma membrane

Domain/homology:

Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Chem-DOQ / : / Glutamate receptor ionotropic, kainate 2

• Biological species: Rattus norvegicus (Norway rat)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
• Authors: Nanao, M.H. / Green, T. / Stern-Bach, Y. / Heinemann, S.F. / Choe, S.
• Citation: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005; Title: Structure of the kainate receptor subunit GluR6 agonist-binding domain complexed with domoic acid.; Authors: Nanao, M.H. / Green, T. / Stern-Bach, Y. / Heinemann, S.F. / Choe, S.

History

Deposition	Dec 17, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.3	Aug 9, 2017	Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Aug 23, 2023	Group: Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

• Remark 300: BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.
• Remark 999: SEQUENCE TRANSMEMBRANE DOMAIN WAS REMOVED AND REPLACED WITH A HYDROPHILIC LINKER.

Assembly

Deposited unit

A: Glutamate receptor, ionotropic kainate 2

B: Glutamate receptor, ionotropic kainate 2

C: Glutamate receptor, ionotropic kainate 2

D: Glutamate receptor, ionotropic kainate 2

E: Glutamate receptor, ionotropic kainate 2

F: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• 215 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	214,939	22
Polymers	210,713	6
Non-polymers	4,226	16
Water	1,405	78

1

A: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author
• 35.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,798	3
Polymers	35,119	1
Non-polymers	679	2
Water	18	1

Symmetry operations:

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

2

B: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author
• 35.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,873	4
Polymers	35,119	1
Non-polymers	754	3
Water	18	1

Symmetry operations:

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

3

C: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author
• 35.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,873	4
Polymers	35,119	1
Non-polymers	754	3
Water	18	1

Symmetry operations:

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

4

D: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author
• 35.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,873	4
Polymers	35,119	1
Non-polymers	754	3
Water	18	1

Symmetry operations:

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

5

E: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author
• 35.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,873	4
Polymers	35,119	1
Non-polymers	754	3
Water	18	1

Symmetry operations:

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

6

F: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by author&software
• 35.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,651	3
Polymers	35,119	1
Non-polymers	533	2
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

7

B: Glutamate receptor, ionotropic kainate 2

D: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by software
• 71.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	71,745	8
Polymers	70,238	2
Non-polymers	1,507	6
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5030 Å2
ΔGint	-5 kcal/mol
Surface area	25950 Å2
Method	PISA

8

A: Glutamate receptor, ionotropic kainate 2

hetero molecules

A: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by software
• 71.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	71,595	6
Polymers	70,238	2
Non-polymers	1,357	4
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,y,-z	1

Calculated values:

Buried area	3930 Å2
ΔGint	1 kcal/mol
Surface area	24170 Å2
Method	PISA

9

C: Glutamate receptor, ionotropic kainate 2

hetero molecules

E: Glutamate receptor, ionotropic kainate 2

hetero molecules

Summary:

• defined by software
• 71.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	71,745	8
Polymers	70,238	2
Non-polymers	1,507	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_455	-x-1/2,y+1/2,-z	1

Calculated values:

Buried area	3380 Å2
ΔGint	0 kcal/mol
Surface area	24330 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	246.360, 106.570, 172.690
Angle α, β, γ (deg.)	90.00, 133.19, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	A
8	1	B
9	1	C
10	1	D
11	1	E
12	1	F
13	1	A
14	1	B
15	1	C
16	1	D
17	1	E
18	1	F
19	1	A
20	1	B
21	1	C
22	1	D
23	1	E
24	1	F
25	1	A
26	1	B
27	1	C
28	1	D
29	1	E
30	1	F
31	1	A
32	1	B
33	1	C
34	1	D
35	1	E
36	1	F
37	1	A
38	1	B
39	1	C
40	1	D
41	1	E
42	1	F
43	1	A
44	1	B
45	1	C
46	1	D
47	1	E
48	1	A
49	1	B
50	1	C
51	1	D
52	1	E
53	1	F
54	1	A
55	1	B
56	1	C
57	1	D
58	1	E
59	1	F
60	1	A
61	1	B
62	1	C
63	1	D
64	1	E
65	1	F
66	1	A
67	1	B
68	1	C
69	1	D
70	1	E
71	1	F
72	1	A
73	1	B
74	1	C
75	1	D
76	1	E
77	1	F
78	1	A
79	1	B
80	1	C
81	1	D
82	1	E
83	1	F

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	ASN	ASN	SER	SER	5	A	A	423 - 427	5 - 9
2	1	ASN	ASN	SER	SER	5	B	B	423 - 427	5 - 9
3	1	ASN	ASN	SER	SER	5	C	C	423 - 427	5 - 9
4	1	ASN	ASN	SER	SER	5	D	D	423 - 427	5 - 9
5	1	ASN	ASN	SER	SER	5	E	E	423 - 427	5 - 9
6	1	ASN	ASN	SER	SER	5	F	F	423 - 427	5 - 9
7	2	LEU	LEU	ARG	ARG	5	A	A	428 - 431	10 - 13
8	2	LEU	LEU	ARG	ARG	5	B	B	428 - 431	10 - 13
9	2	LEU	LEU	ARG	ARG	5	C	C	428 - 431	10 - 13
10	2	LEU	LEU	ARG	ARG	5	D	D	428 - 431	10 - 13
11	2	LEU	LEU	ARG	ARG	5	E	E	428 - 431	10 - 13
12	2	LEU	LEU	ARG	ARG	5	F	F	428 - 431	10 - 13
13	3	SER	SER	VAL	VAL	2	A	A	432 - 444	14 - 26
14	3	SER	SER	VAL	VAL	2	B	B	432 - 444	14 - 26
15	3	SER	SER	VAL	VAL	2	C	C	432 - 444	14 - 26
16	3	SER	SER	VAL	VAL	2	D	D	432 - 444	14 - 26
17	3	SER	SER	VAL	VAL	2	E	E	432 - 444	14 - 26
18	3	SER	SER	VAL	VAL	2	F	F	432 - 444	14 - 26
19	4	LEU	LEU	GLY	GLY	5	A	A	445 - 461	27 - 43
20	4	LEU	LEU	GLY	GLY	5	B	B	445 - 461	27 - 43
21	4	LEU	LEU	GLY	GLY	5	C	C	445 - 461	27 - 43
22	4	LEU	LEU	GLY	GLY	5	D	D	445 - 461	27 - 43
23	4	LEU	LEU	GLY	GLY	5	E	E	445 - 461	27 - 43
24	4	LEU	LEU	GLY	GLY	5	F	F	445 - 461	27 - 43
25	5	GLY	GLY	LYS	LYS	3	A	A	461 - 487	43 - 69
26	5	GLY	GLY	LYS	LYS	3	B	B	461 - 487	43 - 69
27	5	GLY	GLY	LYS	LYS	3	C	C	461 - 487	43 - 69
28	5	GLY	GLY	LYS	LYS	3	D	D	461 - 487	43 - 69
29	5	GLY	GLY	LYS	LYS	3	E	E	461 - 487	43 - 69
30	5	GLY	GLY	LYS	LYS	3	F	F	461 - 487	43 - 69
31	6	TYR	TYR	GLY	GLY	3	A	A	488 - 500	70 - 82
32	6	TYR	TYR	GLY	GLY	3	B	B	488 - 500	70 - 82
33	6	TYR	TYR	GLY	GLY	3	C	C	488 - 500	70 - 82
34	6	TYR	TYR	GLY	GLY	3	D	D	488 - 500	70 - 82
35	6	TYR	TYR	GLY	GLY	3	E	E	488 - 500	70 - 82
36	6	TYR	TYR	GLY	GLY	3	F	F	488 - 500	70 - 82
37	7	MET	MET	LEU	LEU	2	A	A	501 - 541	83 - 123
38	7	MET	MET	LEU	LEU	2	B	B	501 - 541	83 - 123
39	7	MET	MET	LEU	LEU	2	C	C	501 - 541	83 - 123
40	7	MET	MET	LEU	LEU	2	D	D	501 - 541	83 - 123
41	7	MET	MET	LEU	LEU	2	E	E	501 - 541	83 - 123
42	7	MET	MET	LEU	LEU	2	F	F	501 - 541	83 - 123
43	8	ASP	ASP	LYS	LYS	4	A	A	669 - 679	156 - 166
44	8	ASP	ASP	LYS	LYS	4	B	B	669 - 679	156 - 166
45	8	ASP	ASP	LYS	LYS	4	C	C	669 - 679	156 - 166
46	8	ASP	ASP	LYS	LYS	4	D	D	669 - 679	156 - 166
47	8	ASP	ASP	LYS	LYS	4	E	E	669 - 679	156 - 166
48	9	ILE	ILE	LYS	LYS	2	A	A	680 - 695	167 - 182
49	9	ILE	ILE	LYS	LYS	2	B	B	680 - 695	167 - 182
50	9	ILE	ILE	LYS	LYS	2	C	C	680 - 695	167 - 182
51	9	ILE	ILE	LYS	LYS	2	D	D	680 - 695	167 - 182
52	9	ILE	ILE	LYS	LYS	2	E	E	680 - 695	167 - 182
53	9	ILE	ILE	PHE	PHE	2	F	F	680 - 694	167 - 181
54	10	LYS	LYS	VAL	VAL	3	A	A	704 - 716	191 - 203
55	10	LYS	LYS	VAL	VAL	3	B	B	704 - 716	191 - 203
56	10	LYS	LYS	VAL	VAL	3	C	C	704 - 716	191 - 203
57	10	LYS	LYS	VAL	VAL	3	D	D	704 - 716	191 - 203
58	10	LYS	LYS	VAL	VAL	3	E	E	704 - 716	191 - 203
59	10	LYS	LYS	SER	SER	3	F	F	704 - 715	191 - 202
60	11	LEU	LEU	PHE	PHE	2	A	A	717 - 744	204 - 231
61	11	LEU	LEU	PHE	PHE	2	B	B	717 - 744	204 - 231
62	11	LEU	LEU	PHE	PHE	2	C	C	717 - 744	204 - 231
63	11	LEU	LEU	PHE	PHE	2	D	D	717 - 744	204 - 231
64	11	LEU	LEU	PHE	PHE	2	E	E	717 - 744	204 - 231
65	11	LEU	LEU	PHE	PHE	2	F	F	717 - 744	204 - 231
66	12	VAL	VAL	GLY	GLY	3	A	A	745 - 757	232 - 244
67	12	VAL	VAL	GLY	GLY	3	B	B	745 - 757	232 - 244
68	12	VAL	VAL	GLY	GLY	3	C	C	745 - 757	232 - 244
69	12	VAL	VAL	GLY	GLY	3	D	D	745 - 757	232 - 244
70	12	VAL	VAL	GLY	GLY	3	E	E	745 - 757	232 - 244
71	12	VAL	VAL	GLY	GLY	3	F	F	745 - 757	232 - 244
72	13	LEU	LEU	ARG	ARG	4	A	A	758 - 800	245 - 287
73	13	LEU	LEU	ARG	ARG	4	B	B	758 - 800	245 - 287
74	13	LEU	LEU	ARG	ARG	4	C	C	758 - 800	245 - 287
75	13	LEU	LEU	ARG	ARG	4	D	D	758 - 800	245 - 287
76	13	LEU	LEU	ARG	ARG	4	E	E	758 - 800	245 - 287
77	13	LEU	LEU	ARG	ARG	4	F	F	758 - 800	245 - 287
78	14	GLY	GLY	CYS	CYS	5	A	A	801 - 804	288 - 291
79	14	GLY	GLY	CYS	CYS	5	B	B	801 - 804	288 - 291
80	14	GLY	GLY	ASN	ASN	5	C	C	801 - 802	288 - 289
81	14	GLY	GLY	CYS	CYS	5	D	D	801 - 804	288 - 291
82	14	GLY	GLY	GLY	GLY	5	E	E	801	288
83	14	ARG	ARG	ARG	ARG	5	F	F	800	287

Components

#1: Protein

A B C D E F
Glutamate receptor, ionotropic kainate 2 / / Kainate receptor / Glutamate receptor 6 / GluR-6 / GluR6 / Excitatory amino acid receptor 4 / EAA4

Details:

Mass: 35118.863 Da / Num. of mol.: 6
Fragment: Subunit GLUR6 Agonist Binding Domain with the transmembrane domain removed and replaced with a hydrophilic linker
Source method: isolated from a genetically manipulated source
Details: transmembrane domain was removed and replaced with a hydrophilic linker
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Trichoplusia ni (cabbage looper) / References: GenBank: 56280, UniProt: P42260*PLUS

#2: Polysaccharide

T - [G] alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Details:

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor:

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Chemical

A-1103 B-1203 C-1303 D-1403 E-1503 F-1603
ChemComp-DOQ / (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID / (2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID / DOMOIC ACID / Domoic acid

Details:

Mass: 311.330 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₅H₂₁NO₆ / Comment: neurotoxin*YM

#4: Sugar

B-1201 B-1202 C-1301 C-1302 D-1401 D-1402 E-1501 E-1502 F-1601
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine

Details:

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier:

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 4.6 ų/Da / Density % sol: 73 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 ; Details: PIPES, Ammonium Sulphate, Ammonium thiocyanate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
• Detector: Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1998
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.08 Å / Relative weight: 1
• Reflection: Resolution: 3.1→45 Å / Num. obs: 58030 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / R_sym value: 0.118 / Net I/σ(I): 8.7
• Reflection shell: Resolution: 3.1→3.5 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 17019 / R_sym value: 0.42 / % possible all: 94.2

Processing

Software

Name	Version	Classification
REFMAC	5.2.0003	refinement
XDS		data reduction
XDS		data scaling
PHASER	V. 1.2	phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTK

1ftk

Resolution: 3.11→45 Å / Cor.coef. F_o:F_c: 0.864 / Cor.coef. F_o:F_c free: 0.791 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.886 / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.33409	2819	5.1 %	RANDOM
Rwork	0.27545	-	-	-
all	0.27846	-	-	-
obs	0.27846	52826	94.27 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 59.255 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-1.7 Å2	0 Å2	-1 Å2
2-	-	5.91 Å2	0 Å2
3-	-	-	-5.58 Å2

Refinement step

Cycle: LAST / Resolution: 3.11→45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12152	0	282	78	12512

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	12663
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.98	17070
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.828	5	1505
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.017	24.213	553
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.905	15	2316
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.067	15	77
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	1928
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9253
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	6243
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	8702
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	458
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	0.215	0.2	59
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	8
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	1.909	1.5	7550
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.335	2	12193
X-RAY DIFFRACTION	r_scbond_it	0.843	3	5113
X-RAY DIFFRACTION	r_scangle_it	1.469	4.5	4877
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	628	tight positional	0.05	0.05
2	B	628	tight positional	0.05	0.05
3	C	628	tight positional	0.05	0.05
4	D	628	tight positional	0.06	0.05
5	E	628	tight positional	0.05	0.05
6	F	628	tight positional	0.15	0.05
1	A	813	medium positional	0.59	0.5
2	B	813	medium positional	0.57	0.5
3	C	813	medium positional	0.55	0.5
4	D	813	medium positional	0.57	0.5
5	E	813	medium positional	0.62	0.5
6	F	813	medium positional	0.8	0.5
1	A	366	loose positional	1.18	5
2	B	366	loose positional	1.08	5
3	C	366	loose positional	1.1	5
4	D	366	loose positional	1.08	5
5	E	366	loose positional	1.06	5
6	F	366	loose positional	1.69	5
1	A	628	tight thermal	0.08	0.5
2	B	628	tight thermal	0.07	0.5
3	C	628	tight thermal	0.05	0.5
4	D	628	tight thermal	0.05	0.5
5	E	628	tight thermal	0.08	0.5
6	F	628	tight thermal	0.09	0.5
1	A	813	medium thermal	0.51	2
2	B	813	medium thermal	0.44	2
3	C	813	medium thermal	0.37	2
4	D	813	medium thermal	0.35	2
5	E	813	medium thermal	0.4	2
6	F	813	medium thermal	0.73	2
1	A	366	loose thermal	1.88	10
2	B	366	loose thermal	1.44	10
3	C	366	loose thermal	1.55	10
4	D	366	loose thermal	1.57	10
5	E	366	loose thermal	1.49	10
6	F	366	loose thermal	1.96	10

LS refinement shell

Resolution: 3.106→3.273 Å / Total num. of bins used: 10

	Rfactor	Num. reflection	% reflection
Rfree	0.422	364	-
Rwork	0.369	7390	-
obs	-	-	90.48 %