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Found 1 Document (0.508 seconds)

BMRB: 30470

6DHR

NMR Solution structure of Rivi3

Authors

Harvey, P.J., Craik, D.J.

Assembly

Rivi3

Entity

1. Rivi3 (polymer, Thiol state: all disulfide bound), 29 monomers, 3135.748 Da Detail

GLPICGETCL LGKCYTPGCS CRRPVCYKN

Formula weight

3135.748 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

Rinorea virgata

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.3 %, Completeness (bb): 72.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.3 % (256 of 319)	97.6 % (164 of 168)	55.6 % (69 of 124)	85.2 % (23 of 27)
Backbone	72.0 % (121 of 168)	96.6 % (57 of 59)	50.6 % (42 of 83)	84.6 % (22 of 26)
Sidechain	90.9 % (160 of 176)	98.2 % (107 of 109)	78.8 % (52 of 66)	100.0 % (1 of 1)
Aromatic	50.0 % (8 of 16)	100.0 % (8 of 8)	0.0 % (0 of 8)
Methyl	87.5 % (21 of 24)	100.0 % (12 of 12)	75.0 % (9 of 12)

1. entity 1

GLPICGETCL LGKCYTPGCS CRRPVCYKN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1, Details 2.0 mg/mL NA peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	peptide	natural abundance		2.0 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6DHR, Strand ID: A Detail

Release date

2018-06-17

Citation

Discovery and Characterization of Cyclotides from Rinorea Species
Niyomploy, P., Chan, L.Y., Harvey, P.J., Poth, A.G., Colgrave, M.L., Craik, D.J.
J. Nat. Prod. (2018), 81, 2512-2520, PubMed 30387611 , DOI 10.1021/acs.jnatprod.8b00572 , Abstract

Related entities 1. Rivi3, : 1 : 146 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30470_6dhr.nef
Input source #2: Coordindates	6dhr.cif
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)
A:5:CYS:SG	A:19:CYS:SG	oxidized, CA 59.728, CB 49.193 ppm	oxidized, CA 58.037, CB 49.615 ppm	2.023
A:9:CYS:SG	A:21:CYS:SG	oxidized, CB 49.758 ppm	oxidized, CB 41.517 ppm	2.033
A:14:CYS:SG	A:26:CYS:SG	oxidized, CB 44.375 ppm	oxidized, CA 55.789, CB 44.195 ppm	2.026

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---------
GLPICGETCLLGKCYTPGCSCRRPVCYKN
|||||||||||||||||||||||||||||
GLPICGETCLLGKCYTPGCSCRRPVCYKN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	29	0	0	100.0

Content subtype: combined_30470_6dhr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	265		100.0 (chain: A, length: 29)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	371 (1)	noe	100.0 (chain: A, length: 29)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	8 (1)	hbond	20.7 (chain: A, length: 29)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	39 (39)	.	100.0 (chain: A, length: 29)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 173
  - ¹³C chemical shifts: 69
  - ¹⁵N chemical shifts: 23
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	LYS	HZ1	7.478
13	LYS	HZ2	7.478
13	LYS	HZ3	7.478
28	LYS	HZ1	7.609
28	LYS	HZ2	7.609
28	LYS	HZ3	7.609

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	166	98.8
¹³C chemical shifts	124	69	55.6
¹⁵N chemical shifts	29	23	79.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	58	98.3
¹³C chemical shifts	58	17	29.3
¹⁵N chemical shifts	26	22	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	108	99.1
¹³C chemical shifts	66	52	78.8
¹⁵N chemical shifts	3	1	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0
¹³C chemical shifts	12	9	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%
- Total number of restraints: 371
- Weight of restraints: 1.0 (371)
- Potential type of restraints: square-well-parabolic (371)
- Range of distance target values: 2.16, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 20.7%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 1.0, 1.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%
- Total number of restraints: 39
- Total number of restraints per polymer type: 39
- Weight of restraints: 1.0 (39)
- Potential type of restraints: square-well-parabolic (39)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PLANT PROTEIN, cyclotide cyclic peptide

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Found 1 Document (0.508 seconds)

BMRB: 30470

Sample

Related entities 1. Rivi3, : 1 : 146 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail