BMRBj - BMREntryMaster

Found 1 Document (0.598 seconds)

BMRB: 34392

6RC7

NMR structure of cytotoxin 3 from Naja kaouthia in solution, major form

Authors

Dubinnyi, M.A., Dubovskii, P.V., Utkin, Y.N., Arseniev, A.S.

Assembly

Cytotoxin 3

Entity

1. Cytotoxin 3 (polymer, Thiol state: all disulfide bound), 60 monomers, 6717.130 Da Detail

LKCNKLIPLA YKTCPAGKNL CYKMFMVSNK TVPVKRGCID ACPKNSLLVK YVCCNTDRCN

Formula weight

6717.13 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS21:SG
2	disulfide	sing	1:CYS14:SG	1:CYS38:SG
3	disulfide	sing	1:CYS42:SG	1:CYS53:SG
4	disulfide	sing	1:CYS54:SG	1:CYS59:SG

Source organism

Naja kaouthia

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.5 %, Completeness (bb): 83.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (623 of 712)	97.9 % (367 of 375)	72.7 % (200 of 275)	90.3 % (56 of 62)
Backbone	83.0 % (292 of 352)	97.5 % (115 of 118)	68.5 % (122 of 178)	98.2 % (55 of 56)
Sidechain	93.1 % (389 of 418)	98.1 % (252 of 257)	87.7 % (136 of 155)	16.7 % (1 of 6)
Aromatic	50.0 % (17 of 34)	100.0 % (17 of 17)	0.0 % (0 of 17)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. entity 1

LKCNKLIPLA YKTCPAGKNL CYKMFMVSNK TVPVKRGCID ACPKNSLLVK YVCCNTDRCN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) bar, Temperature 303 (±1) K, pH 4.00 (±0.05), Details 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

Sample #2

Solvent system 100% D2O, Pressure 1 (±0.01) bar, Temperature 303 (±1) K, pH 4.00 (±0.05), Details 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
4	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6RC7, Strand ID: A Detail

Release date

2020-05-03

Citation

The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions
Dubinnyi, M.A., Dubovskii, P.V., Starkov, V.G., Utkin, Y.N.
Biochem. Biophys. Res. Commun. (2021), 558, 141-146, PubMed 33915327 , DOI 10.1016/j.bbrc.2021.04.069 , Abstract

Related entities 1. Cytotoxin 3, : 1 : 1 : 4 : 194 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) bar, Temperature 303 (±1) K, pH 4.00 (±0.05), Details 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

2 2D DQF-COSY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

3 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

4 2D ROESY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

5 2D 1H-13C HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

6 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

7 2D 1H-13C HSQC-TOCSY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
2	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

8 2D DQF-COSY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 (±0.01) bar, Temperature 303 (±1) K, pH 4.0 (±0.05), Details 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
4	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

9 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
4	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

10 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Cytotoxin 3 from Naja kaouthia	natural abundance		3 mM
4	Cytotoxin 2 from Naja kaouthia	natural abundance		2 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34392_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)
1:3:CYS:SG	1:21:CYS:SG	oxidized, CA 49.424, CB 38.5 ppm	oxidized, CA 49.316, CB 36.279 ppm	n/a
1:14:CYS:SG	1:38:CYS:SG	oxidized, CA 49.431, CB 34.839 ppm	oxidized, CA 53.725, CB 44.803 ppm	n/a
1:42:CYS:SG	1:53:CYS:SG	oxidized, CA 52.424, CB 39.425 ppm	oxidized, CA 52.314, CB 46.744 ppm	n/a
1:54:CYS:SG	1:59:CYS:SG	oxidized, CA 52.82, CB 43.559 ppm	oxidized, CA 53.907, CB 43.581 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34392_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	691		100.0 (chain: 1, length: 60)
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: 60, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 439
  - ¹³C chemical shifts: 196
  - ¹⁵N chemical shifts: 56
- 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	7.748
23	LYS	HZ2	7.748
23	LYS	HZ3	7.748

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	375	372	99.2
¹³C chemical shifts	275	196	71.3
¹⁵N chemical shifts	64	56	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	117	99.2
¹³C chemical shifts	120	60	50.0
¹⁵N chemical shifts	56	55	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	257	255	99.2
¹³C chemical shifts	155	136	87.7
¹⁵N chemical shifts	8	1	12.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	32	94.1
¹³C chemical shifts	34	32	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	0	0.0

Keywords Cobra snake venom, TOXIN, Three-finger toxin, beta-structure, cytolytic peptide, disulfide-rich protein

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Found 1 Document (0.598 seconds)

BMRB: 34392

Sample #1

Sample #2

Related entities 1. Cytotoxin 3, : 1 : 1 : 4 : 194 entities Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail