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BMRB: 30323

5WOV

Solution NMR structure of cyclotide MCoTI-I

Authors

Schroeder, C.I., Kwon, S.

Assembly

Two inhibitor peptide topologies 2

Entity

1. Two inhibitor peptide topologies 2 (polymer, Thiol state: not present), 34 monomers, 3504.961 Da Detail

GGVCPKILQR CRRDSDCPGA CICRGNGYCG SGSD

Formula weight

3504.961 Da

Source organism

Momordica cochinchinensis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.2 %, Completeness (bb): 82.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (300 of 340)	98.9 % (178 of 180)	71.4 % (90 of 126)	94.1 % (32 of 34)
Backbone	82.5 % (165 of 200)	98.6 % (72 of 73)	66.3 % (63 of 95)	93.8 % (30 of 32)
Sidechain	97.0 % (162 of 167)	99.1 % (106 of 107)	93.1 % (54 of 58)	100.0 % (2 of 2)
Aromatic	50.0 % (4 of 8)	100.0 % (4 of 4)	0.0 % (0 of 4)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. Two inhibitor peptide topologies 2

GGVCPKILQR CRRDSDCPGA CICRGNGYCG SGSD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0, Details 0.5 mM NA MCoTI-I, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	MCoTI-I	natural abundance		0.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0, Details 0.5 mM NA MCoTI-I, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	MCoTI-I	natural abundance		0.5 mM

Release date

2017-08-17

Citation

Targeted Delivery of Cyclotides via Conjugation to a Nanobody
Kwon, S., Duarte, J.N., Li, Z., Ling, J.J., Cheneval, O., Durek, T., Schroeder, C.I., Craik, D.J., Ploegh, H.L.
ACS Chem. Biol. (2018), 13, 2973-2980, PubMed 30248263 , DOI 10.1021/acschembio.8b00653 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30324 released on 2017-08-17
Title Solution NMR structure of cyclotide MCoTI-I

Related entities 1. Two inhibitor peptide topologies 2, : 1 : 3 : 49 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30323_5wov.nef
Input source #2: Coordindates	5wov.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	True (see coodinates for details)
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:4:CYS:SG	A:21:CYS:SG	oxidized, CA 54.879, CB 43.714 ppm	oxidized, CA 58.739, CB 48.237 ppm	2.028
A:11:CYS:SG	A:23:CYS:SG	oxidized, CA 56.748, CB 50.658 ppm	oxidized, CA 57.626, CB 40.79 ppm	2.033
A:17:CYS:SG	A:29:CYS:SG	oxidized, CA 54.805, CB 43.255 ppm	oxidized, CA 58.256, CB 43.567 ppm	2.043

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:34:ASP:C	1:1:GLY:N	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30----
GGVCPKILQRCRRDSDCPGACICRGNGYCGSGSD
||||||||||||||||||||||||||||||||||
GGVCPKILQRCRRDSDCPGACICRGNGYCGSGSD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_30323_5wov.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	306		100.0 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	376 (1)	noe	97.1 (chain: A, length: 34)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	12 (1)	hbond	29.4 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	46 (46)	.	85.3 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 181
  - ¹³C chemical shifts: 88
  - ¹⁵N chemical shifts: 37
- 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)
6	LYS	HZ1	7.545
6	LYS	HZ2	7.545
6	LYS	HZ3	7.545
6	LYS	NZ	126.786

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	177	98.3
¹³C chemical shifts	126	88	69.8
¹⁵N chemical shifts	38	36	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	71	97.3
¹³C chemical shifts	68	34	50.0
¹⁵N chemical shifts	32	30	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	106	99.1
¹³C chemical shifts	58	54	93.1
¹⁵N chemical shifts	6	6	100.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	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: 34, Sequence coverage: 97.1%
- Total number of restraints: 376
- Weight of restraints: 1.0 (376)
- Potential type of restraints: square-well-parabolic (376)
- Range of distance target values: 1.31, 4.22 (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: 34, Sequence coverage: 29.4%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - 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: 34, Sequence coverage: 85.3%
- Total number of restraints: 46
- Total number of restraints per polymer type: 46
- Weight of restraints: 1.0 (46)
- Potential type of restraints: square-well-parabolic (46)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PLANT PROTEIN, cyclic cystine knot, cyclotide, plant peptide

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Found 1 Document (0.59 seconds)

BMRB: 30323

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Two inhibitor peptide topologies 2, : 1 : 3 : 49 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail