PDB-1yce: Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter ...

Basic information

• Entry: Database: PDB / ID: 1yce
• Title: Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus
• Components: subunit c
• Keywords: MEMBRANE PROTEIN / ATP Synthase / Na binding site

Function / homology

Function:

sodium ion transport / : / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane

Domain/homology:

F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha

Component:

NONAN-1-OL / : / ATP synthase subunit c, sodium ion specific

• Biological species: Ilyobacter tartaricus (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
• Authors: Meier, T. / Polzer, P. / Diederichs, K. / Welte, W. / Dimroth, P.
• Citation: Journal: Science / Year: 2005; Title: Structure of the rotor ring of F-Type Na+-ATPase from Ilyobacter tartaricus.; Authors: Meier, T. / Polzer, P. / Diederichs, K. / Welte, W. / Dimroth, P.

History

Deposition	Dec 22, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _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_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.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_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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

• Remark 600: HETEROGEN THE AUTHORS HAD ZWITTERGENT 3-12 IN THE CRYSTALLIZATION DROP BUT AS THIS IS MUCH BIGGER THAN THE DENSITY, THE AUTHORS CALLED IT F09, NONAN-1-OL, BECAUSE IT EXACTLY MATCHES THE DENSITY. THE AUTHORS STATE THAT IF THE DENSITY COMES FROM ZWITTERGENT 3-12, THEN THE REST OF IT SEEMS TO BE DISORDERED.
• Remark 650: HELIX AUTHOR DETERMINED HELIX RECORDS

Assembly

Deposited unit

A: subunit c

B: subunit c

C: subunit c

D: subunit c

E: subunit c

F: subunit c

G: subunit c

H: subunit c

I: subunit c

J: subunit c

K: subunit c

L: subunit c

M: subunit c

N: subunit c

O: subunit c

P: subunit c

Q: subunit c

R: subunit c

S: subunit c

T: subunit c

U: subunit c

V: subunit c

a: subunit c

b: subunit c

c: subunit c

d: subunit c

e: subunit c

f: subunit c

g: subunit c

h: subunit c

i: subunit c

j: subunit c

k: subunit c

l: subunit c

m: subunit c

n: subunit c

o: subunit c

p: subunit c

q: subunit c

r: subunit c

s: subunit c

t: subunit c

u: subunit c

v: subunit c

hetero molecules

Summary:

• 395 kDa, 44 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	394,528	132
Polymers	387,169	44
Non-polymers	7,359	88
Water	9,242	513

1

A: subunit c

B: subunit c

C: subunit c

D: subunit c

E: subunit c

F: subunit c

G: subunit c

H: subunit c

I: subunit c

J: subunit c

K: subunit c

hetero molecules

Summary:

• defined by author&software
• 98.6 kDa, 11 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,632	33
Polymers	96,792	11
Non-polymers	1,840	22
Water	198	11

Symmetry operations:

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

Calculated values:

Buried area	47450 Å2
ΔGint	-480 kcal/mol
Surface area	25480 Å2
Method	PISA

2

L: subunit c

M: subunit c

N: subunit c

O: subunit c

P: subunit c

Q: subunit c

R: subunit c

S: subunit c

T: subunit c

U: subunit c

V: subunit c

hetero molecules

Summary:

• defined by author&software
• 98.6 kDa, 11 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,632	33
Polymers	96,792	11
Non-polymers	1,840	22
Water	198	11

Symmetry operations:

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

Calculated values:

Buried area	47330 Å2
ΔGint	-481 kcal/mol
Surface area	25680 Å2
Method	PISA

3

a: subunit c

b: subunit c

c: subunit c

d: subunit c

e: subunit c

f: subunit c

g: subunit c

h: subunit c

i: subunit c

j: subunit c

k: subunit c

hetero molecules

Summary:

• defined by author&software
• 98.6 kDa, 11 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,632	33
Polymers	96,792	11
Non-polymers	1,840	22
Water	198	11

Symmetry operations:

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

Calculated values:

Buried area	47160 Å2
ΔGint	-483 kcal/mol
Surface area	25740 Å2
Method	PISA

4

l: subunit c

m: subunit c

n: subunit c

o: subunit c

p: subunit c

q: subunit c

r: subunit c

s: subunit c

t: subunit c

u: subunit c

v: subunit c

hetero molecules

Summary:

• defined by author&software
• 98.6 kDa, 11 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,632	33
Polymers	96,792	11
Non-polymers	1,840	22
Water	198	11

Symmetry operations:

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

Calculated values:

Buried area	47390 Å2
ΔGint	-483 kcal/mol
Surface area	25630 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	147.700, 140.000, 153.000
Angle α, β, γ (deg.)	90.00, 118.40, 90.00
Int Tables number	4
Space group name H-M	P1211

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	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L
13	1	M
14	1	N
15	1	O
16	1	P
17	1	Q
18	1	R
19	1	S
20	1	T
21	1	U
22	1	V
23	1	a
24	1	b
25	1	c
26	1	d
27	1	e
28	1	f
29	1	g
30	1	h
31	1	i
32	1	j
33	1	k
34	1	l
35	1	m
36	1	n
37	1	o
38	1	p
39	1	q
40	1	r
41	1	s
42	1	t
43	1	u
44	1	v
45	1	A
46	1	B
47	1	C
48	1	D
49	1	E
50	1	F
51	1	G
52	1	H
53	1	I
54	1	J
55	1	K
56	1	L
57	1	M
58	1	N
59	1	O
60	1	P
61	1	Q
62	1	R
63	1	S
64	1	T
65	1	U
66	1	V
67	1	a
68	1	b
69	1	c
70	1	d
71	1	e
72	1	f
73	1	g
74	1	h
75	1	i
76	1	j
77	1	k
78	1	l
79	1	m
80	1	n
81	1	o
82	1	p
83	1	q
84	1	r
85	1	s
86	1	t
87	1	u
88	1	v
89	1	A
90	1	B
91	1	C
92	1	D
93	1	E
94	1	F
95	1	G
96	1	H
97	1	I
98	1	J
99	1	K
100	1	L
101	1	M
102	1	N
103	1	O
104	1	P
105	1	Q
106	1	R
107	1	S
108	1	T
109	1	U
110	1	V
111	1	a
112	1	b
113	1	c
114	1	d
115	1	e
116	1	f
117	1	g
118	1	h
119	1	i
120	1	j
121	1	k
122	1	l
123	1	m
124	1	n
125	1	o
126	1	p
127	1	q
128	1	r
129	1	s
130	1	t
131	1	u
132	1	v
133	1	A
134	1	B
135	1	C
136	1	D
137	1	E
138	1	F
139	1	G
140	1	H
141	1	I
142	1	J
143	1	K
144	1	L
145	1	M
146	1	N
147	1	O
148	1	P
149	1	Q
150	1	R
151	1	S
152	1	T
153	1	U
154	1	V
155	1	a
156	1	b
157	1	c
158	1	d
159	1	e
160	1	f
161	1	g
162	1	h
163	1	i
164	1	j
165	1	k
166	1	l
167	1	m
168	1	n
169	1	o
170	1	p
171	1	q
172	1	r
173	1	s
174	1	t
175	1	u
176	1	v

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	VAL	VAL	2	A	A	1 - 40	1 - 40
2	1	MET	MET	VAL	VAL	2	B	B	1 - 40	1 - 40
3	1	MET	MET	VAL	VAL	2	C	C	1 - 40	1 - 40
4	1	MET	MET	VAL	VAL	2	D	D	1 - 40	1 - 40
5	1	MET	MET	VAL	VAL	2	E	E	1 - 40	1 - 40
6	1	MET	MET	VAL	VAL	2	F	F	1 - 40	1 - 40
7	1	MET	MET	VAL	VAL	2	G	G	1 - 40	1 - 40
8	1	MET	MET	VAL	VAL	2	H	H	1 - 40	1 - 40
9	1	MET	MET	VAL	VAL	2	I	I	1 - 40	1 - 40
10	1	MET	MET	VAL	VAL	2	J	J	1 - 40	1 - 40
11	1	MET	MET	VAL	VAL	2	K	K	1 - 40	1 - 40
12	1	MET	MET	VAL	VAL	2	L	L	1 - 40	1 - 40
13	1	MET	MET	VAL	VAL	2	M	M	1 - 40	1 - 40
14	1	MET	MET	VAL	VAL	2	N	N	1 - 40	1 - 40
15	1	MET	MET	VAL	VAL	2	O	O	1 - 40	1 - 40
16	1	MET	MET	VAL	VAL	2	P	P	1 - 40	1 - 40
17	1	MET	MET	VAL	VAL	2	Q	Q	1 - 40	1 - 40
18	1	MET	MET	VAL	VAL	2	R	R	1 - 40	1 - 40
19	1	MET	MET	VAL	VAL	2	S	S	1 - 40	1 - 40
20	1	MET	MET	VAL	VAL	2	T	T	1 - 40	1 - 40
21	1	MET	MET	VAL	VAL	2	U	U	1 - 40	1 - 40
22	1	MET	MET	VAL	VAL	2	V	V	1 - 40	1 - 40
23	1	MET	MET	VAL	VAL	2	a	W	1 - 40	1 - 40
24	1	MET	MET	VAL	VAL	2	b	X	1 - 40	1 - 40
25	1	MET	MET	VAL	VAL	2	c	Y	1 - 40	1 - 40
26	1	MET	MET	VAL	VAL	2	d	Z	1 - 40	1 - 40
27	1	MET	MET	VAL	VAL	2	e	AA	1 - 40	1 - 40
28	1	MET	MET	VAL	VAL	2	f	BA	1 - 40	1 - 40
29	1	MET	MET	VAL	VAL	2	g	CA	1 - 40	1 - 40
30	1	MET	MET	VAL	VAL	2	h	DA	1 - 40	1 - 40
31	1	MET	MET	VAL	VAL	2	i	EA	1 - 40	1 - 40
32	1	MET	MET	VAL	VAL	2	j	FA	1 - 40	1 - 40
33	1	MET	MET	VAL	VAL	2	k	GA	1 - 40	1 - 40
34	1	MET	MET	VAL	VAL	2	l	HA	1 - 40	1 - 40
35	1	MET	MET	VAL	VAL	2	m	IA	1 - 40	1 - 40
36	1	MET	MET	VAL	VAL	2	n	JA	1 - 40	1 - 40
37	1	MET	MET	VAL	VAL	2	o	KA	1 - 40	1 - 40
38	1	MET	MET	VAL	VAL	2	p	LA	1 - 40	1 - 40
39	1	MET	MET	VAL	VAL	2	q	MA	1 - 40	1 - 40
40	1	MET	MET	VAL	VAL	2	r	NA	1 - 40	1 - 40
41	1	MET	MET	VAL	VAL	2	s	OA	1 - 40	1 - 40
42	1	MET	MET	VAL	VAL	2	t	PA	1 - 40	1 - 40
43	1	MET	MET	VAL	VAL	2	u	QA	1 - 40	1 - 40
44	1	MET	MET	VAL	VAL	2	v	RA	1 - 40	1 - 40
45	2	ILE	ILE	GLY	GLY	2	A	A	53 - 89	53 - 89
46	2	ILE	ILE	GLY	GLY	2	B	B	53 - 89	53 - 89
47	2	ILE	ILE	GLY	GLY	2	C	C	53 - 89	53 - 89
48	2	ILE	ILE	GLY	GLY	2	D	D	53 - 89	53 - 89
49	2	ILE	ILE	GLY	GLY	2	E	E	53 - 89	53 - 89
50	2	ILE	ILE	GLY	GLY	2	F	F	53 - 89	53 - 89
51	2	ILE	ILE	GLY	GLY	2	G	G	53 - 89	53 - 89
52	2	ILE	ILE	GLY	GLY	2	H	H	53 - 89	53 - 89
53	2	ILE	ILE	GLY	GLY	2	I	I	53 - 89	53 - 89
54	2	ILE	ILE	GLY	GLY	2	J	J	53 - 89	53 - 89
55	2	ILE	ILE	GLY	GLY	2	K	K	53 - 89	53 - 89
56	2	ILE	ILE	GLY	GLY	2	L	L	53 - 89	53 - 89
57	2	ILE	ILE	GLY	GLY	2	M	M	53 - 89	53 - 89
58	2	ILE	ILE	GLY	GLY	2	N	N	53 - 89	53 - 89
59	2	ILE	ILE	GLY	GLY	2	O	O	53 - 89	53 - 89
60	2	ILE	ILE	GLY	GLY	2	P	P	53 - 89	53 - 89
61	2	ILE	ILE	GLY	GLY	2	Q	Q	53 - 89	53 - 89
62	2	ILE	ILE	GLY	GLY	2	R	R	53 - 89	53 - 89
63	2	ILE	ILE	GLY	GLY	2	S	S	53 - 89	53 - 89
64	2	ILE	ILE	GLY	GLY	2	T	T	53 - 89	53 - 89
65	2	ILE	ILE	GLY	GLY	2	U	U	53 - 89	53 - 89
66	2	ILE	ILE	GLY	GLY	2	V	V	53 - 89	53 - 89
67	2	ILE	ILE	GLY	GLY	2	a	W	53 - 89	53 - 89
68	2	ILE	ILE	GLY	GLY	2	b	X	53 - 89	53 - 89
69	2	ILE	ILE	GLY	GLY	2	c	Y	53 - 89	53 - 89
70	2	ILE	ILE	GLY	GLY	2	d	Z	53 - 89	53 - 89
71	2	ILE	ILE	GLY	GLY	2	e	AA	53 - 89	53 - 89
72	2	ILE	ILE	GLY	GLY	2	f	BA	53 - 89	53 - 89
73	2	ILE	ILE	GLY	GLY	2	g	CA	53 - 89	53 - 89
74	2	ILE	ILE	GLY	GLY	2	h	DA	53 - 89	53 - 89
75	2	ILE	ILE	GLY	GLY	2	i	EA	53 - 89	53 - 89
76	2	ILE	ILE	GLY	GLY	2	j	FA	53 - 89	53 - 89
77	2	ILE	ILE	GLY	GLY	2	k	GA	53 - 89	53 - 89
78	2	ILE	ILE	GLY	GLY	2	l	HA	53 - 89	53 - 89
79	2	ILE	ILE	GLY	GLY	2	m	IA	53 - 89	53 - 89
80	2	ILE	ILE	GLY	GLY	2	n	JA	53 - 89	53 - 89
81	2	ILE	ILE	GLY	GLY	2	o	KA	53 - 89	53 - 89
82	2	ILE	ILE	GLY	GLY	2	p	LA	53 - 89	53 - 89
83	2	ILE	ILE	GLY	GLY	2	q	MA	53 - 89	53 - 89
84	2	ILE	ILE	GLY	GLY	2	r	NA	53 - 89	53 - 89
85	2	ILE	ILE	GLY	GLY	2	s	OA	53 - 89	53 - 89
86	2	ILE	ILE	GLY	GLY	2	t	PA	53 - 89	53 - 89
87	2	ILE	ILE	GLY	GLY	2	u	QA	53 - 89	53 - 89
88	2	ILE	ILE	GLY	GLY	2	v	RA	53 - 89	53 - 89
89	3	NA	NA	NA	NA	4	A	SA	201
90	3	NA	NA	NA	NA	4	B	UA	201
91	3	NA	NA	NA	NA	4	C	WA	201
92	3	NA	NA	NA	NA	4	D	YA	201
93	3	NA	NA	NA	NA	4	E	AB	201
94	3	NA	NA	NA	NA	4	F	CB	201
95	3	NA	NA	NA	NA	4	G	EB	201
96	3	NA	NA	NA	NA	4	H	GB	201
97	3	NA	NA	NA	NA	4	I	IB	201
98	3	NA	NA	NA	NA	4	J	KB	201
99	3	NA	NA	NA	NA	4	K	MB	201
100	3	NA	NA	NA	NA	4	L	OB	201
101	3	NA	NA	NA	NA	4	M	QB	201
102	3	NA	NA	NA	NA	4	N	SB	201
103	3	NA	NA	NA	NA	4	O	UB	201
104	3	NA	NA	NA	NA	4	P	WB	201
105	3	NA	NA	NA	NA	4	Q	YB	201
106	3	NA	NA	NA	NA	4	R	AC	201
107	3	NA	NA	NA	NA	4	S	CC	201
108	3	NA	NA	NA	NA	4	T	EC	201
109	3	NA	NA	NA	NA	4	U	GC	201
110	3	NA	NA	NA	NA	4	V	IC	201
111	3	NA	NA	NA	NA	4	a	KC	201
112	3	NA	NA	NA	NA	4	b	MC	201
113	3	NA	NA	NA	NA	4	c	OC	201
114	3	NA	NA	NA	NA	4	d	QC	201
115	3	NA	NA	NA	NA	4	e	SC	201
116	3	NA	NA	NA	NA	4	f	UC	201
117	3	NA	NA	NA	NA	4	g	WC	201
118	3	NA	NA	NA	NA	4	h	YC	201
119	3	NA	NA	NA	NA	4	i	AD	201
120	3	NA	NA	NA	NA	4	j	CD	201
121	3	NA	NA	NA	NA	4	k	ED	201
122	3	NA	NA	NA	NA	4	l	GD	201
123	3	NA	NA	NA	NA	4	m	ID	201
124	3	NA	NA	NA	NA	4	n	KD	201
125	3	NA	NA	NA	NA	4	o	MD	201
126	3	NA	NA	NA	NA	4	p	OD	201
127	3	NA	NA	NA	NA	4	q	QD	201
128	3	NA	NA	NA	NA	4	r	SD	201
129	3	NA	NA	NA	NA	4	s	UD	201
130	3	NA	NA	NA	NA	4	t	WD	201
131	3	NA	NA	NA	NA	4	u	YD	201
132	3	NA	NA	NA	NA	4	v	AE	201
133	4	F09	F09	F09	F09	4	A	TA	314
134	4	F09	F09	F09	F09	4	B	VA	314
135	4	F09	F09	F09	F09	4	C	XA	314
136	4	F09	F09	F09	F09	4	D	ZA	314
137	4	F09	F09	F09	F09	4	E	BB	314
138	4	F09	F09	F09	F09	4	F	DB	314
139	4	F09	F09	F09	F09	4	G	FB	314
140	4	F09	F09	F09	F09	4	H	HB	314
141	4	F09	F09	F09	F09	4	I	JB	314
142	4	F09	F09	F09	F09	4	J	LB	314
143	4	F09	F09	F09	F09	4	K	NB	314
144	4	F09	F09	F09	F09	4	L	PB	314
145	4	F09	F09	F09	F09	4	M	RB	314
146	4	F09	F09	F09	F09	4	N	TB	314
147	4	F09	F09	F09	F09	4	O	VB	314
148	4	F09	F09	F09	F09	4	P	XB	314
149	4	F09	F09	F09	F09	4	Q	ZB	314
150	4	F09	F09	F09	F09	4	R	BC	314
151	4	F09	F09	F09	F09	4	S	DC	314
152	4	F09	F09	F09	F09	4	T	FC	314
153	4	F09	F09	F09	F09	4	U	HC	314
154	4	F09	F09	F09	F09	4	V	JC	314
155	4	F09	F09	F09	F09	4	a	LC	314
156	4	F09	F09	F09	F09	4	b	NC	314
157	4	F09	F09	F09	F09	4	c	PC	314
158	4	F09	F09	F09	F09	4	d	RC	314
159	4	F09	F09	F09	F09	4	e	TC	314
160	4	F09	F09	F09	F09	4	f	VC	314
161	4	F09	F09	F09	F09	4	g	XC	314
162	4	F09	F09	F09	F09	4	h	ZC	314
163	4	F09	F09	F09	F09	4	i	BD	314
164	4	F09	F09	F09	F09	4	j	DD	314
165	4	F09	F09	F09	F09	4	k	FD	314
166	4	F09	F09	F09	F09	4	l	HD	314
167	4	F09	F09	F09	F09	4	m	JD	314
168	4	F09	F09	F09	F09	4	n	LD	314
169	4	F09	F09	F09	F09	4	o	ND	314
170	4	F09	F09	F09	F09	4	p	PD	314
171	4	F09	F09	F09	F09	4	q	RD	314
172	4	F09	F09	F09	F09	4	r	TD	314
173	4	F09	F09	F09	F09	4	s	VD	314
174	4	F09	F09	F09	F09	4	t	XD	314
175	4	F09	F09	F09	F09	4	u	ZD	314
176	4	F09	F09	F09	F09	4	v	BE	314

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R S ...
subunit c

Details:

Mass: 8799.304 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Ilyobacter tartaricus (bacteria) / References: GenBank: 22266794, UniProt: Q8KRV3*PLUS

#2: Chemical

A-201 B-201 C-201 D-201 E-201 F-201 G-201 H-201 I-201 J-201 K-201 L-201 M-201 N-201 O-201 P-201 Q-201 R-201 S-201 T-201 ...
ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Na

#3: Chemical

A-314 B-314 C-314 D-314 E-314 F-314 G-314 H-314 I-314 J-314 K-314 L-314 M-314 N-314 O-314 P-314 Q-314 R-314 S-314 T-314 ...
ChemComp-F09 / NONAN-1-OL

Details:

Mass: 144.254 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C₉H₂₀O

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 513 / 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: 3.5 ų/Da / Density % sol: 65 %
• Crystal grow: Temperature: 290 K / Method: vapor diffusion / pH: 4.5 ; Details: 15% PEG400, 0.1M NaAc, pH 4.5, VAPOR DIFFUSION, temperature 290K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
• Detector: Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2004
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9756 Å / Relative weight: 1
• Reflection: Resolution: 2.4→10 Å / Num. all: 209310 / Num. obs: 198822 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / R_merge(I) obs: 0.183 / R_sym value: 0.175 / Net I/σ(I): 10
• Reflection shell: Resolution: 2.4→2.5 Å / Redundancy: 8 % / R_merge(I) obs: 0.635 / Mean I/σ(I) obs: 3.3 / R_sym value: 0.589 / % possible all: 95.2

Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data scaling
PHASER		phasing

Refinement

Resolution: 2.4→10 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.936 / SU B: 18.132 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24595	10461	5 %	RANDOM
Rwork	0.20055	-	-	-
obs	0.20282	198822	99.43 %	-

• 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: 44.851 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-4.09 Å2	0 Å2	1.35 Å2
2-	-	2.77 Å2	0 Å2
3-	-	-	2.6 Å2

Refinement step

Cycle: LAST / Resolution: 2.4→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27104	0	484	513	28101

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	27808
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	28116
X-RAY DIFFRACTION	r_angle_refined_deg	1.91	2.007	37576
X-RAY DIFFRACTION	r_angle_other_deg	1.005	3	64900
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.157	5	3872
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.786	25.333	660
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.467	15	4312
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.67	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	4664
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	31020
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4928
X-RAY DIFFRACTION	r_nbd_refined	0.248	0.2	7667
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	27022
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	14174
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	15209
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	585
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.148	0.2	101
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.237	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.264	0.2	79
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.223	0.2	13
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	0.717	1.5	19140
X-RAY DIFFRACTION	r_mcbond_other	0.214	1.5	8360
X-RAY DIFFRACTION	r_mcangle_it	1.257	2	30184
X-RAY DIFFRACTION	r_scbond_it	2.255	3	8800
X-RAY DIFFRACTION	r_scangle_it	3.68	4.5	7392
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	447	tight positional	0.01	0.05
2	B	447	tight positional	0.01	0.05
3	C	447	tight positional	0.01	0.05
4	D	447	tight positional	0.01	0.05
5	E	447	tight positional	0.01	0.05
6	F	447	tight positional	0.01	0.05
7	G	447	tight positional	0.01	0.05
8	H	447	tight positional	0.01	0.05
9	I	447	tight positional	0.01	0.05
10	J	447	tight positional	0.01	0.05
11	K	447	tight positional	0.01	0.05
12	L	447	tight positional	0.01	0.05
13	M	447	tight positional	0.01	0.05
14	N	447	tight positional	0.01	0.05
15	O	447	tight positional	0.01	0.05
16	P	447	tight positional	0.01	0.05
17	Q	447	tight positional	0.01	0.05
18	R	447	tight positional	0.01	0.05
19	S	447	tight positional	0.01	0.05
20	T	447	tight positional	0.01	0.05
21	U	447	tight positional	0.01	0.05
22	V	447	tight positional	0.01	0.05
23	b	447	tight positional	0.01	0.05
24	c	447	tight positional	0.01	0.05
25	d	447	tight positional	0.01	0.05
26	e	447	tight positional	0.01	0.05
27	f	447	tight positional	0.01	0.05
28	g	447	tight positional	0.01	0.05
29	h	447	tight positional	0.01	0.05
30	i	447	tight positional	0.01	0.05
31	j	447	tight positional	0.01	0.05
32	k	447	tight positional	0.01	0.05
33	l	447	tight positional	0.01	0.05
34	m	447	tight positional	0.01	0.05
35	n	447	tight positional	0.01	0.05
36	o	447	tight positional	0.01	0.05
37	p	447	tight positional	0.01	0.05
38	q	447	tight positional	0.01	0.05
39	r	447	tight positional	0.01	0.05
40	s	447	tight positional	0.01	0.05
41	t	447	tight positional	0.01	0.05
42	u	447	tight positional	0.01	0.05
43	v	447	tight positional	0.01	0.05
44	A	447	tight positional	0.01	0.05
1	A	652	medium positional	0.08	0.5
2	B	652	medium positional	0.09	0.5
3	C	652	medium positional	0.09	0.5
4	D	652	medium positional	0.08	0.5
5	E	652	medium positional	0.08	0.5
6	F	652	medium positional	0.08	0.5
7	G	652	medium positional	0.08	0.5
8	H	652	medium positional	0.08	0.5
9	I	652	medium positional	0.12	0.5
10	J	652	medium positional	0.09	0.5
11	K	652	medium positional	0.12	0.5
12	L	652	medium positional	0.08	0.5
13	M	652	medium positional	0.08	0.5
14	N	652	medium positional	0.09	0.5
15	O	652	medium positional	0.08	0.5
16	P	652	medium positional	0.09	0.5
17	Q	652	medium positional	0.08	0.5
18	R	652	medium positional	0.08	0.5
19	S	652	medium positional	0.08	0.5
20	T	652	medium positional	0.08	0.5
21	U	652	medium positional	0.08	0.5
22	V	652	medium positional	0.08	0.5
23	e	652	medium positional	0.08	0.5
24	f	652	medium positional	0.09	0.5
25	g	652	medium positional	0.09	0.5
26	h	652	medium positional	0.08	0.5
27	i	652	medium positional	0.08	0.5
28	j	652	medium positional	0.08	0.5
29	k	652	medium positional	0.08	0.5
30	l	652	medium positional	0.08	0.5
31	m	652	medium positional	0.12	0.5
32	n	652	medium positional	0.09	0.5
33	o	652	medium positional	0.12	0.5
34	p	652	medium positional	0.08	0.5
35	q	652	medium positional	0.08	0.5
36	r	652	medium positional	0.09	0.5
37	s	652	medium positional	0.08	0.5
38	t	652	medium positional	0.09	0.5
39	u	652	medium positional	0.08	0.5
40	v	652	medium positional	0.08	0.5
41	A	652	medium positional	0.08	0.5
42	B	652	medium positional	0.08	0.5
43	C	652	medium positional	0.08	0.5
44	D	652	medium positional	0.08	0.5
1	A	447	tight thermal	0.41	5
2	B	447	tight thermal	0.45	5
3	C	447	tight thermal	0.37	5
4	D	447	tight thermal	0.41	5
5	E	447	tight thermal	0.37	5
6	F	447	tight thermal	0.39	5
7	G	447	tight thermal	0.4	5
8	H	447	tight thermal	0.4	5
9	I	447	tight thermal	0.45	5
10	J	447	tight thermal	0.56	5
11	K	447	tight thermal	0.47	5
12	L	447	tight thermal	0.47	5
13	M	447	tight thermal	0.43	5
14	N	447	tight thermal	0.43	5
15	O	447	tight thermal	0.53	5
16	P	447	tight thermal	0.47	5
17	Q	447	tight thermal	0.42	5
18	R	447	tight thermal	0.44	5
19	S	447	tight thermal	0.46	5
20	T	447	tight thermal	0.42	5
21	U	447	tight thermal	0.46	5
22	V	447	tight thermal	0.44	5
23	e	447	tight thermal	0.41	5
24	f	447	tight thermal	0.45	5
25	g	447	tight thermal	0.37	5
26	h	447	tight thermal	0.41	5
27	i	447	tight thermal	0.37	5
28	j	447	tight thermal	0.39	5
29	k	447	tight thermal	0.4	5
30	l	447	tight thermal	0.4	5
31	m	447	tight thermal	0.45	5
32	n	447	tight thermal	0.56	5
33	o	447	tight thermal	0.47	5
34	p	447	tight thermal	0.47	5
35	q	447	tight thermal	0.43	5
36	r	447	tight thermal	0.43	5
37	s	447	tight thermal	0.53	5
38	t	447	tight thermal	0.47	5
39	u	447	tight thermal	0.42	5
40	v	447	tight thermal	0.44	5
41	A	447	tight thermal	0.46	5
42	B	447	tight thermal	0.42	5
43	C	447	tight thermal	0.46	5
44	D	447	tight thermal	0.44	5
1	A	652	medium thermal	1.18	20
2	B	652	medium thermal	1.01	20
3	C	652	medium thermal	1.01	20
4	D	652	medium thermal	1.12	20
5	E	652	medium thermal	0.98	20
6	F	652	medium thermal	0.96	20
7	G	652	medium thermal	1.07	20
8	H	652	medium thermal	1.14	20
9	I	652	medium thermal	1.1	20
10	J	652	medium thermal	1.17	20
11	K	652	medium thermal	1.17	20
12	L	652	medium thermal	1	20
13	M	652	medium thermal	1.08	20
14	N	652	medium thermal	1.06	20
15	O	652	medium thermal	1.31	20
16	P	652	medium thermal	1.14	20
17	Q	652	medium thermal	0.95	20
18	R	652	medium thermal	1.21	20
19	S	652	medium thermal	0.94	20
20	T	652	medium thermal	1.01	20
21	U	652	medium thermal	1.15	20
22	V	652	medium thermal	1.02	20
23	e	652	medium thermal	1.18	20
24	f	652	medium thermal	1.01	20
25	g	652	medium thermal	1.01	20
26	h	652	medium thermal	1.12	20
27	i	652	medium thermal	0.98	20
28	j	652	medium thermal	0.96	20
29	k	652	medium thermal	1.07	20
30	l	652	medium thermal	1.14	20
31	m	652	medium thermal	1.1	20
32	n	652	medium thermal	1.17	20
33	o	652	medium thermal	1.17	20
34	p	652	medium thermal	1	20
35	q	652	medium thermal	1.08	20
36	r	652	medium thermal	1.06	20
37	s	652	medium thermal	1.31	20
38	t	652	medium thermal	1.14	20
39	u	652	medium thermal	0.95	20
40	v	652	medium thermal	1.21	20
41	A	652	medium thermal	0.94	20
42	B	652	medium thermal	1.01	20
43	C	652	medium thermal	1.15	20
44	D	652	medium thermal	1.02	20

LS refinement shell

Resolution: 2.4→2.459 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.357	691	-
Rwork	0.298	13177	-
obs	-	-	93.16 %

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	1.9484	0.0286	0.058	0.6598	-0.0233	0.8022	-0.0364	0.0778	0.2872	-0.0169	0.0246	0.0071	-0.0412	0.0404	0.0118	-0.0982	-0.0242	0.0032	-0.1547	0.0192	-0.0954	5.0263	23.0604	19.3241
2	1.8821	0.0528	-0.1157	0.6812	-0.0021	0.8562	-0.0333	0.1036	0.0213	-0.0339	0.0218	-0.0247	0.016	-0.0638	0.0115	-0.1178	-0.0342	-0.0041	-0.179	0.031	-0.1874	-67.8849	9.1795	20.2115
3	2.2308	0.1214	0.0037	0.6755	0.0096	0.8062	-0.0598	-0.0193	-0.0334	-0.0111	0.0273	0.0232	-0.0033	0.0635	0.0324	-0.0776	-0.0424	-0.0068	-0.2506	0.0532	-0.2403	31.5204	90.6324	47.2022
4	2.0349	-0.1088	-0.0701	0.6732	0.022	0.8628	-0.0463	-0.0158	-0.3669	-0.0203	0.0264	-0.0032	0.0494	-0.0882	0.0198	-0.0597	-0.0441	-0.0091	-0.2091	0.0433	-0.1349	-41.375	76.7271	47.8003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 89	1 - 89
2	X-RAY DIFFRACTION	1	B	B	1 - 89	1 - 89
3	X-RAY DIFFRACTION	1	C	C	1 - 89	1 - 89
4	X-RAY DIFFRACTION	1	D	D	1 - 89	1 - 89
5	X-RAY DIFFRACTION	1	E	E	1 - 89	1 - 89
6	X-RAY DIFFRACTION	1	F	F	1 - 89	1 - 89
7	X-RAY DIFFRACTION	1	G	G	1 - 89	1 - 89
8	X-RAY DIFFRACTION	1	H	H	1 - 89	1 - 89
9	X-RAY DIFFRACTION	1	I	I	1 - 89	1 - 89
10	X-RAY DIFFRACTION	1	J	J	1 - 89	1 - 89
11	X-RAY DIFFRACTION	1	K	K	1 - 89	1 - 89
12	X-RAY DIFFRACTION	2	L	L	1 - 89	1 - 89
13	X-RAY DIFFRACTION	2	M	M	1 - 89	1 - 89
14	X-RAY DIFFRACTION	2	N	N	1 - 89	1 - 89
15	X-RAY DIFFRACTION	2	O	O	1 - 89	1 - 89
16	X-RAY DIFFRACTION	2	P	P	1 - 89	1 - 89
17	X-RAY DIFFRACTION	2	Q	Q	1 - 89	1 - 89
18	X-RAY DIFFRACTION	2	R	R	1 - 89	1 - 89
19	X-RAY DIFFRACTION	2	S	S	1 - 89	1 - 89
20	X-RAY DIFFRACTION	2	T	T	1 - 89	1 - 89
21	X-RAY DIFFRACTION	2	U	U	1 - 89	1 - 89
22	X-RAY DIFFRACTION	2	V	V	1 - 89	1 - 89
23	X-RAY DIFFRACTION	3	a	W	1 - 89	1 - 89
24	X-RAY DIFFRACTION	3	b	X	1 - 89	1 - 89
25	X-RAY DIFFRACTION	3	c	Y	1 - 89	1 - 89
26	X-RAY DIFFRACTION	3	d	Z	1 - 89	1 - 89
27	X-RAY DIFFRACTION	3	e	AA	1 - 89	1 - 89
28	X-RAY DIFFRACTION	3	f	BA	1 - 89	1 - 89
29	X-RAY DIFFRACTION	3	g	CA	1 - 89	1 - 89
30	X-RAY DIFFRACTION	3	h	DA	1 - 89	1 - 89
31	X-RAY DIFFRACTION	3	i	EA	1 - 89	1 - 89
32	X-RAY DIFFRACTION	3	j	FA	1 - 89	1 - 89
33	X-RAY DIFFRACTION	3	k	GA	1 - 89	1 - 89
34	X-RAY DIFFRACTION	4	l	HA	1 - 89	1 - 89
35	X-RAY DIFFRACTION	4	m	IA	1 - 89	1 - 89
36	X-RAY DIFFRACTION	4	n	JA	1 - 89	1 - 89
37	X-RAY DIFFRACTION	4	o	KA	1 - 89	1 - 89
38	X-RAY DIFFRACTION	4	p	LA	1 - 89	1 - 89
39	X-RAY DIFFRACTION	4	q	MA	1 - 89	1 - 89
40	X-RAY DIFFRACTION	4	r	NA	1 - 89	1 - 89
41	X-RAY DIFFRACTION	4	s	OA	1 - 89	1 - 89
42	X-RAY DIFFRACTION	4	t	PA	1 - 89	1 - 89
43	X-RAY DIFFRACTION	4	u	QA	1 - 89	1 - 89
44	X-RAY DIFFRACTION	4	v	RA	1 - 89	1 - 89