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Found 1 Document (0.589 seconds)

BMRB: 30813

7KPD

NMR Solution Structure of Acyclotide ribe 31

Authors

Harvey, P.J., Craik, D.J., Dang, T.T.

Assembly

Acyclotide ribe 31

Entity

1. Acyclotide ribe 31 (polymer, Thiol state: all disulfide bound), 29 monomers, 3136.776 Da Detail

AIPCGESCVY IPCISVVIGC SCRNKVCYR

Formula weight

3136.776 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS20:SG
2	disulfide	sing	1:CYS8:SG	1:CYS22:SG
3	disulfide	sing	1:CYS13:SG	1:CYS27:SG

Source organism

Rinorea bengalensis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.9 %, Completeness (bb): 74.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (251 of 318)	96.3 % (157 of 163)	55.2 % (69 of 125)	83.3 % (25 of 30)
Backbone	74.1 % (126 of 170)	98.3 % (57 of 58)	52.9 % (45 of 85)	88.9 % (24 of 27)
Sidechain	85.7 % (150 of 175)	95.2 % (100 of 105)	73.1 % (49 of 67)	33.3 % (1 of 3)
Aromatic	37.5 % (6 of 16)	75.0 % (6 of 8)	0.0 % (0 of 8)
Methyl	79.4 % (27 of 34)	94.1 % (16 of 17)	64.7 % (11 of 17)

1. entity 1

AIPCGESCVY IPCISVVIGC SCRNKVCYR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mM ribe 31, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	ribe 31	natural abundance		1.0 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 7KPD, Strand ID: A Detail

Release date

2020-12-08

Citation

In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis
Dang, T.T., Chan, L.Y., Tombling, B.J., Harvey, P.J., Gilding, E.K., Craik, D.J.
J. Nat. Prod. (2021), 84, 395-407, PubMed 33570395 , DOI 10.1021/acs.jnatprod.0c01065 , Abstract

Related entities 1. Acyclotide ribe 31, : 1 : 123 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30813_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)
1:4:CYS:SG	1:20:CYS:SG	oxidized, CA 57.266, CB 45.026 ppm	oxidized, CB 46.6 ppm	n/a
1:8:CYS:SG	1:22:CYS:SG	oxidized, CA 55.392, CB 46.002 ppm	oxidized, CB 41.089 ppm	n/a
1:13:CYS:SG	1:27:CYS:SG	oxidized, CA 57.016, CB 40.632 ppm	oxidized, CA 55.703, CB 43.314 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30813_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	283		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: 189
  - ¹³C chemical shifts: 69
  - ¹⁵N chemical shifts: 25
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	163	157	96.3
¹³C chemical shifts	125	69	55.2
¹⁵N chemical shifts	30	25	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	57	98.3
¹³C chemical shifts	58	20	34.5
¹⁵N chemical shifts	27	24	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	100	95.2
¹³C chemical shifts	67	49	73.1
¹⁵N chemical shifts	3	1	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	16	94.1
¹³C chemical shifts	17	11	64.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	6	75.0
¹³C chemical shifts	8	0	0.0

Keywords ANTIMICROBIAL PROTEIN

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Found 1 Document (0.589 seconds)

BMRB: 30813

Sample

Related entities 1. Acyclotide ribe 31, : 1 : 123 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail