BMRBj - BMREntryMaster

Found 1 Document (0.49 seconds)

BMRB: 31102

8TYI

NMR structure of L5pG ([p23W, G24W]kalata B1)

Authors

Tian, S., Craik, D.J., Conan, K.W.

Assembly

Kalata-B1

Entity

1. Kalata-B1 (polymer, Thiol state: all disulfide bound), 29 monomers, 2787.177 Da Detail

GLPVCGETCV GGTCNTPGCT CSXGVCTRN

Formula weight

2787.177 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS19:SG
2	disulfide	sing	1:CYS9:SG	1:CYS21:SG
3	disulfide	sing	1:CYS14:SG	1:CYS26:SG

Source organism

Oldenlandia affinis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 159, ¹³C: 67, ¹⁵N: 28 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err
1	1	1	GLY	HA2	H	3.845	0.001
2	1	1	GLY	HA3	H	3.846	0.000
3	1	1	GLY	CA	C	45.564	0.000
4	1	2	LEU	H	H	8.565	0.001
5	1	2	LEU	HA	H	4.631	0.003
6	1	2	LEU	HB2	H	1.460	0.003
7	1	2	LEU	HB3	H	1.586	0.004
8	1	2	LEU	HG	H	1.696	0.003
9	1	2	LEU	HD11	H	0.931	0.003
10	1	2	LEU	HD12	H	0.931	0.003
11	1	2	LEU	HD13	H	0.931	0.003
12	1	2	LEU	HD21	H	0.931	0.003
13	1	2	LEU	HD22	H	0.931	0.003
14	1	2	LEU	HD23	H	0.931	0.003
15	1	2	LEU	CA	C	55.876	0.000
16	1	2	LEU	CB	C	44.294	0.020
17	1	2	LEU	CG	C	29.728	0.000
18	1	2	LEU	N	N	122.764	0.000
19	1	3	PRO	HA	H	4.455	0.002
20	1	3	PRO	HB2	H	2.317	0.003
21	1	3	PRO	HB3	H	2.098	0.000
22	1	3	PRO	HG2	H	2.052	0.001
23	1	3	PRO	HG3	H	1.848	0.001
24	1	3	PRO	HD2	H	3.887	0.001
25	1	3	PRO	HD3	H	3.617	0.001
26	1	3	PRO	CA	C	65.728	0.000
27	1	3	PRO	CB	C	34.680	0.000
28	1	3	PRO	CD	C	53.247	0.004
29	1	4	VAL	H	H	8.280	0.003
30	1	4	VAL	HA	H	4.087	0.003
31	1	4	VAL	HB	H	2.089	0.002
32	1	4	VAL	HG11	H	0.970	0.002
33	1	4	VAL	HG12	H	0.970	0.002
34	1	4	VAL	HG13	H	0.970	0.002
35	1	4	VAL	HG21	H	0.970	0.002
36	1	4	VAL	HG22	H	0.970	0.002
37	1	4	VAL	HG23	H	0.970	0.002
38	1	4	VAL	CA	C	64.980	0.000
39	1	4	VAL	CB	C	35.237	0.001
40	1	4	VAL	CG1	C	23.053	0.000
41	1	4	VAL	N	N	120.682	0.000
42	1	5	CYS	H	H	8.490	0.001
43	1	5	CYS	HA	H	4.953	0.005
44	1	5	CYS	HB2	H	2.845	0.002
45	1	5	CYS	HB3	H	2.845	0.002
46	1	5	CYS	CA	C	56.897	0.000
47	1	5	CYS	CB	C	42.035	0.040
48	1	5	CYS	N	N	121.649	0.000
49	1	6	GLY	H	H	8.117	0.002
50	1	6	GLY	HA2	H	3.739	0.003
51	1	6	GLY	HA3	H	4.199	0.003
52	1	6	GLY	CA	C	48.304	0.010
53	1	6	GLY	N	N	108.395	0.000
54	1	7	GLU	H	H	8.198	0.003
55	1	7	GLU	HA	H	4.454	0.002
56	1	7	GLU	HB2	H	2.196	0.003
57	1	7	GLU	HB3	H	2.069	0.003
58	1	7	GLU	HG2	H	2.640	0.003
59	1	7	GLU	HG3	H	2.544	0.005
60	1	7	GLU	CA	C	58.908	0.000
61	1	7	GLU	CB	C	31.255	0.023
62	1	7	GLU	CG	C	36.237	0.007
63	1	7	GLU	N	N	118.702	0.000
64	1	8	THR	H	H	8.416	0.002
65	1	8	THR	HA	H	4.502	0.004
66	1	8	THR	HB	H	4.260	0.002
67	1	8	THR	HG21	H	1.354	0.002
68	1	8	THR	HG22	H	1.354	0.002
69	1	8	THR	HG23	H	1.354	0.002
70	1	8	THR	CA	C	65.025	0.000
71	1	8	THR	CB	C	72.413	0.000
72	1	8	THR	CG2	C	24.696	0.000
73	1	8	THR	N	N	114.020	0.000
74	1	9	CYS	H	H	8.051	0.003
75	1	9	CYS	HA	H	4.730	0.008
76	1	9	CYS	HB2	H	3.059	0.002
77	1	9	CYS	HB3	H	3.059	0.002
78	1	9	CYS	CA	C	58.067	0.000
79	1	9	CYS	CB	C	47.481	0.000
80	1	9	CYS	N	N	119.349	0.000
81	1	10	VAL	H	H	8.593	0.002
82	1	10	VAL	HA	H	4.106	0.003
83	1	10	VAL	HB	H	1.994	0.002
84	1	10	VAL	HG11	H	0.936	0.009
85	1	10	VAL	HG12	H	0.936	0.009
86	1	10	VAL	HG13	H	0.936	0.009
87	1	10	VAL	HG21	H	0.936	0.009
88	1	10	VAL	HG22	H	0.936	0.009
89	1	10	VAL	HG23	H	0.936	0.009
90	1	10	VAL	CA	C	65.782	0.000
91	1	10	VAL	CB	C	35.213	0.027
92	1	10	VAL	CG1	C	23.437	0.000
93	1	10	VAL	N	N	123.528	0.000
94	1	11	GLY	H	H	8.973	0.002
95	1	11	GLY	HA2	H	3.882	0.003
96	1	11	GLY	HA3	H	3.972	0.002
97	1	11	GLY	CA	C	48.947	0.000
98	1	11	GLY	N	N	115.316	0.000
99	1	12	GLY	H	H	8.241	0.002
100	1	12	GLY	HA2	H	3.881	0.001
101	1	12	GLY	HA3	H	4.182	0.001
102	1	12	GLY	CA	C	48.047	0.010
103	1	12	GLY	N	N	105.594	0.000
104	1	13	THR	H	H	7.729	0.002
105	1	13	THR	HA	H	4.729	0.009
106	1	13	THR	HB	H	4.139	0.005
107	1	13	THR	HG21	H	1.153	0.001
108	1	13	THR	HG22	H	1.153	0.001
109	1	13	THR	HG23	H	1.153	0.001
110	1	13	THR	CA	C	63.262	0.000
111	1	13	THR	CB	C	74.123	0.000
112	1	13	THR	CG2	C	23.716	0.000
113	1	13	THR	N	N	113.084	0.000
114	1	14	CYS	H	H	8.718	0.001
115	1	14	CYS	HA	H	4.820	0.009
116	1	14	CYS	HB2	H	3.203	0.002
117	1	14	CYS	HB3	H	2.853	0.002
118	1	14	CYS	CA	C	58.472	0.000
119	1	14	CYS	CB	C	47.689	0.029
120	1	14	CYS	N	N	121.162	0.000
121	1	15	ASN	H	H	8.748	0.002
122	1	15	ASN	HA	H	4.657	0.004
123	1	15	ASN	HB2	H	2.831	0.003
124	1	15	ASN	HB3	H	2.837	0.006
125	1	15	ASN	HD21	H	7.603	0.005
126	1	15	ASN	HD22	H	6.865	0.007
127	1	15	ASN	CA	C	56.650	0.000
128	1	15	ASN	CB	C	41.463	0.023
129	1	15	ASN	N	N	121.210	0.000
130	1	15	ASN	ND2	N	112.357	0.015
131	1	16	THR	H	H	7.695	0.005
132	1	16	THR	HA	H	4.604	0.005
133	1	16	THR	HB	H	3.989	0.002
134	1	16	THR	HG21	H	1.266	0.003
135	1	16	THR	HG22	H	1.266	0.003
136	1	16	THR	HG23	H	1.266	0.003
137	1	16	THR	CA	C	62.973	0.000
138	1	16	THR	CB	C	73.179	0.000
139	1	16	THR	CG2	C	24.050	0.000
140	1	16	THR	N	N	117.896	0.000
141	1	17	PRO	HA	H	4.327	0.002
142	1	17	PRO	HB2	H	2.336	0.006
143	1	17	PRO	HB3	H	2.123	0.005
144	1	17	PRO	HG2	H	1.994	0.002
145	1	17	PRO	HG3	H	1.898	0.001
146	1	17	PRO	HD2	H	4.089	0.002
147	1	17	PRO	HD3	H	3.721	0.002
148	1	17	PRO	CA	C	66.416	0.000
149	1	17	PRO	CB	C	34.637	0.000
150	1	17	PRO	CD	C	54.289	0.010
151	1	18	GLY	H	H	8.734	0.003
152	1	18	GLY	HA2	H	3.714	0.004
153	1	18	GLY	HA3	H	4.237	0.003
154	1	18	GLY	CA	C	47.661	0.020
155	1	18	GLY	N	N	110.647	0.000
156	1	19	CYS	H	H	7.667	0.003
157	1	19	CYS	HA	H	5.333	0.003
158	1	19	CYS	HB2	H	2.999	0.005
159	1	19	CYS	HB3	H	2.772	0.002
160	1	19	CYS	CA	C	56.168	0.000
161	1	19	CYS	CB	C	46.359	0.010
162	1	19	CYS	N	N	117.256	0.000
163	1	20	THR	H	H	9.515	0.002
164	1	20	THR	HA	H	4.590	0.002
165	1	20	THR	HB	H	3.977	0.003
166	1	20	THR	HG21	H	1.119	0.002
167	1	20	THR	HG22	H	1.119	0.002
168	1	20	THR	HG23	H	1.119	0.002
169	1	20	THR	CA	C	63.369	0.000
170	1	20	THR	CB	C	74.040	0.000
171	1	20	THR	CG2	C	23.474	0.000
172	1	20	THR	N	N	117.926	0.000
173	1	21	CYS	H	H	8.906	0.002
174	1	21	CYS	HA	H	4.546	0.002
175	1	21	CYS	HB2	H	3.046	0.003
176	1	21	CYS	HB3	H	2.791	0.003
177	1	21	CYS	CA	C	59.931	0.000
178	1	21	CYS	CB	C	44.685	0.017
179	1	21	CYS	N	N	125.845	0.000
180	1	22	SER	H	H	9.095	0.002
181	1	22	SER	HA	H	5.071	0.003
182	1	22	SER	HB2	H	3.838	0.004
183	1	22	SER	HB3	H	3.758	0.001
184	1	22	SER	CA	C	57.521	0.000
185	1	22	SER	CB	C	66.422	0.000
186	1	22	SER	N	N	127.178	0.000
187	1	23	DPR	CA	C	67.398	0.000
188	1	23	DPR	CB	C	34.187	0.000
189	1	23	DPR	CD	C	53.464	0.011
190	1	23	DPR	HA	H	4.340	0.004
191	1	23	DPR	HB2	H	2.387	0.002
192	1	23	DPR	HB3	H	2.127	0.000
193	1	23	DPR	HD2	H	3.913	0.002
194	1	23	DPR	HD3	H	3.804	0.003
195	1	23	DPR	HG2	H	2.057	0.003
196	1	23	DPR	HG3	H	1.970	0.003
197	1	24	GLY	H	H	7.663	0.004
198	1	24	GLY	HA2	H	3.609	0.002
199	1	24	GLY	HA3	H	4.225	0.009
200	1	24	GLY	CA	C	48.427	0.014
201	1	24	GLY	N	N	101.751	0.000
202	1	25	VAL	H	H	7.813	0.003
203	1	25	VAL	HA	H	4.532	0.004
204	1	25	VAL	HB	H	1.939	0.003
205	1	25	VAL	HG11	H	0.871	0.004
206	1	25	VAL	HG12	H	0.871	0.004
207	1	25	VAL	HG13	H	0.871	0.004
208	1	25	VAL	HG21	H	0.871	0.004
209	1	25	VAL	HG22	H	0.871	0.004
210	1	25	VAL	HG23	H	0.871	0.004
211	1	25	VAL	CA	C	63.420	0.000
212	1	25	VAL	CB	C	38.309	0.003
213	1	25	VAL	CG1	C	23.572	0.000
214	1	25	VAL	N	N	121.024	0.000
215	1	26	CYS	H	H	8.889	0.002
216	1	26	CYS	HA	H	5.002	0.005
217	1	26	CYS	HB2	H	2.730	0.006
218	1	26	CYS	HB3	H	3.372	0.003
219	1	26	CYS	CA	C	59.267	0.000
220	1	26	CYS	CB	C	46.565	0.004
221	1	26	CYS	N	N	124.845	0.000
222	1	27	THR	H	H	9.771	0.003
223	1	27	THR	HA	H	4.739	0.011
224	1	27	THR	HB	H	4.134	0.003
225	1	27	THR	HG21	H	1.223	0.002
226	1	27	THR	HG22	H	1.223	0.002
227	1	27	THR	HG23	H	1.223	0.002
228	1	27	THR	CA	C	63.238	0.000
229	1	27	THR	CB	C	74.122	0.000
230	1	27	THR	CG2	C	23.544	0.000
231	1	27	THR	N	N	122.099	0.000
232	1	28	ARG	H	H	8.629	0.002
233	1	28	ARG	HA	H	4.682	0.004
234	1	28	ARG	HB2	H	1.895	0.003
235	1	28	ARG	HB3	H	1.777	0.003
236	1	28	ARG	HG2	H	1.728	0.003
237	1	28	ARG	HD2	H	3.253	0.001
238	1	28	ARG	HE	H	7.274	0.002
239	1	28	ARG	CA	C	59.539	0.000
240	1	28	ARG	CB	C	33.345	0.011
241	1	28	ARG	CG	C	30.026	0.000
242	1	28	ARG	CD	C	46.168	0.000
243	1	28	ARG	N	N	124.834	0.000
244	1	28	ARG	NE	N	124.520	0.000
245	1	29	ASN	H	H	8.319	0.002
246	1	29	ASN	HA	H	4.549	0.006
247	1	29	ASN	HB2	H	2.720	0.004
248	1	29	ASN	HB3	H	2.722	0.002
249	1	29	ASN	HD21	H	7.480	0.004
250	1	29	ASN	HD22	H	6.802	0.007
251	1	29	ASN	CA	C	56.332	0.000
252	1	29	ASN	CB	C	42.198	0.000
253	1	29	ASN	N	N	126.332	0.000
254	1	29	ASN	ND2	N	111.063	0.002

Release date

2023-10-01

Citation

Nucleation of a key beta-turn promotes cyclotide oxidative folding
Tian, S., de Veer, S.J., Durek, T., Wang, C.K., Craik, D.J.
J. Biol. Chem. (2024), 107125-107125, PubMed 38432638 , DOI 10.1016/j.jbc.2024.107125 , Abstract

Related entities 1. Kalata-B1, : 1 : 11 : 128 entities Detail

Experiments performed 4 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	L5pG	natural abundance		2 mg/mL

#	Name	Isotope labeling	Type	Concentration
1	L5pG	natural abundance		2 mg/mL

#	Name	Isotope labeling	Type	Concentration
1	L5pG	natural abundance		2 mg/mL

#	Name	Isotope labeling	Type	Concentration
1	L5pG	natural abundance		2 mg/mL

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr31102_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:5:CYS:SG	1:19:CYS:SG	oxidized, CA 56.897, CB 42.035 ppm	oxidized, CA 56.168, CB 46.359 ppm	n/a
1:9:CYS:SG	1:21:CYS:SG	oxidized, CA 58.067, CB 47.481 ppm	oxidized, CA 59.931, CB 44.685 ppm	n/a
1:14:CYS:SG	1:26:CYS:SG	oxidized, CA 58.472, CB 47.689 ppm	oxidized, CA 59.267, CB 46.565 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	23	DPR	D-PROLINE	Assigned chemical shifts

Content subtype: bmr31102_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	254		100.0 (chain: 1, length: 29)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 29, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 159
  - ¹³C chemical shifts: 67
  - ¹⁵N chemical shifts: 28
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID
23	DPR

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	129	126	97.7
¹³C chemical shifts	99	64	64.6
¹⁵N chemical shifts	29	28	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	59	98.3
¹³C chemical shifts	56	28	50.0
¹⁵N chemical shifts	26	25	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	67	97.1
¹³C chemical shifts	43	36	83.7
¹⁵N chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	13	100.0
¹³C chemical shifts	13	8	61.5

Keywords UNKNOWN FUNCTION, beta-turn, cyclotide, cystine knot, oxidative folding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.49 seconds)

BMRB: 31102

Related entities 1. Kalata-B1, : 1 : 11 : 128 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail