BMRBj - BMREntryMaster

Found 1 Document (0.487 seconds)

BMRB: 30938

7RIH

hyen D solution structure

Authors

Du, Q., Huang, Y.H., Craik, D.J., Wang, C.K.

Assembly

D-hDM1, Cyclotide hyen-D

Entity

1. D-hDM1, Cyclotide hyen-D (polymer, Thiol state: all disulfide bound), 30 monomers, 3179.752 Da Detail

GFPCGESCVY IPCFTAAIGC SCKSKVCYKN

Formula weight

3179.752 Da

Entity Connection

disulfide 3, covalent 1 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
4	covalent	sing	1:GLY1:N	1:ASN30:C

Source organism

Afrohybanthus enneaspermus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.3 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.3 % (270 of 328)	96.4 % (163 of 169)	62.3 % (81 of 130)	89.7 % (26 of 29)
Backbone	80.7 % (142 of 176)	98.4 % (60 of 61)	65.5 % (57 of 87)	89.3 % (25 of 28)
Sidechain	86.0 % (154 of 179)	95.4 % (103 of 108)	71.4 % (50 of 70)	100.0 % (1 of 1)
Aromatic	38.9 % (14 of 36)	77.8 % (14 of 18)	0.0 % (0 of 18)
Methyl	86.4 % (19 of 22)	90.9 % (10 of 11)	81.8 % (9 of 11)

1. entity 1

GFPCGESCVY IPCFTAAIGC SCKSKVCYKN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5, Details 4 mg/mL hyen D, 90 % H2O, 10 % D2O, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	hyen D	natural abundance	4 mg/mL
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Release date

2021-08-22

Citation

Mutagenesis of bracelet cyclotide hyen D reveals functionally and structurally critical residues for membrane binding and cytotoxicity
Du, Q., Huang, Y.H., Wang, C.K., Kaas, Q., Craik, D.J.
J. Biol. Chem. (2022), 298, 101822-101822, PubMed 35283188 , DOI 10.1016/j.jbc.2022.101822 , Abstract

Related entities 1. D-hDM1, Cyclotide hyen-D, : 1 : 1 : 1 : 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	bmr30938_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	True (see coordinates for details)
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 55.05, CB 45.448 ppm	oxidized, CA 57.731, CB 48.378 ppm	n/a
1:8:CYS:SG	1:22:CYS:SG	oxidized, CA 55.243, CB 46.106 ppm	oxidized, CA 56.43, CB 41.433 ppm	n/a
1:13:CYS:SG	1:27:CYS:SG	oxidized, CA 57.204, CB 41.194 ppm	oxidized, CA 55.831, CB 43.174 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30938_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	296		100.0 (chain: 1, length: 30)
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: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 191
  - ¹³C chemical shifts: 80
  - 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
23	LYS	HZ1	7.365
23	LYS	HZ2	7.365
23	LYS	HZ3	7.365
25	LYS	HZ1	7.538
25	LYS	HZ2	7.538
25	LYS	HZ3	7.538
29	LYS	HZ1	7.577
29	LYS	HZ2	7.577
29	LYS	HZ3	7.577

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	162	95.9
¹³C chemical shifts	130	80	61.5
¹⁵N chemical shifts	29	25	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	59	96.7
¹³C chemical shifts	60	30	50.0
¹⁵N chemical shifts	28	24	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	103	95.4
¹³C chemical shifts	70	50	71.4
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	10	90.9
¹³C chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	14	77.8
¹³C chemical shifts	18	0	0.0

Keywords PLANT PROTEIN, cyclotides

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Found 1 Document (0.487 seconds)

BMRB: 30938

Sample

Related entities 1. D-hDM1, Cyclotide hyen-D, : 1 : 1 : 1 : 1 : 123 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail