BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	98.8 % (720 of 729)	99.2 % (381 of 384)	98.2 % (278 of 283)	98.4 % (61 of 62)
Backbone	97.5 % (349 of 358)	97.5 % (117 of 120)	97.2 % (176 of 181)	98.2 % (56 of 57)
Sidechain	100.0 % (430 of 430)	100.0 % (264 of 264)	100.0 % (161 of 161)	100.0 % (5 of 5)
Aromatic	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. entity 1

MLKCNKLVPI AYKTCPEGKN LCYKMFMMSD LTIPVKRGCI DVCPKNSLLV KYVCCNTDRC N

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 101325 (±100) Pa, Temperature 303 (±0.2) K, pH 6.5 (±0.1), Details 1 mM U-99% 13C; U-99% 15N recombinant cytotoxin-I, 95 v/v non-labeled H2O, 5 v/v 99.9% 2H D2O, 3 uM non-labeled NaOH, 1 uM non-labeled HCl, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: 2.58 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: 2.58 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: 3.3 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5T8A, Strand ID: A Detail

Release date

2017-09-12

Citation

Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?
Dubovskii, P.V., Dubinnyi, M.A., Konshina, A.G., Kazakova, E.D., Sorokoumova, G.M., Ilyasova, T.M., Shulepko, M.A., Chertkova, R.V., Lyukmanova, E.N., Dolgikh, D.A., Arseniev, A.S., Efremov, R.G.
Biochemistry (2017), 56, 4468-4477, PubMed 28749688 , DOI 10.1021/acs.biochem.7b00453 , Abstract

Related entities 1. Cytotoxin 1, : 1 : 1 : 6 : 193 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 101325 (±100) Pa, Temperature 303 (±0.2) K, pH 6.5 (±0.1), Details 1 mM U-99% 13C; U-99% 15N recombinant cytotoxin-I, 95 v/v non-labeled H2O, 5 v/v 99.9% 2H D2O, 3 uM non-labeled NaOH, 1 uM non-labeled HCl, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

3 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

4 3D HN(COCA)CB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 101325 (±100) Pa, Temperature 303 (±0.2) K, pH 6.5 (±0.1), Details 1 mM U-99% 13C; U-99% 15N recombinant cytotoxin-I, 95 v/v non-labeled H2O, 5 v/v 99.9% 2H D2O, 3 uM non-labeled NaOH, 1 uM non-labeled HCl, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

10 1D-watergate

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	[U-99.9% 2H]	5 (±0.1) v/v
2	H2O	natural abundance	95 (±0.1) v/v
3	HCl	natural abundance	1 (±0.1) uM
4	NaOH	natural abundance	3 (±0.1) uM
5	recombinant cytotoxin-I	[U-99% 13C; U-99% 15N]	1 (±0.1) mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30172_5t8a.nef
Input source #2: Coordindates	5t8a.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:3:CYS:SG	A:21:CYS:SG	oxidized, CA 49.345, CB 38.39 ppm	oxidized, CA 49.173, CB 36.243 ppm	2.015
A:14:CYS:SG	A:38:CYS:SG	oxidized, CA 49.313, CB 34.888 ppm	oxidized, CA 53.344, CB 44.753 ppm	2.03
A:42:CYS:SG	A:53:CYS:SG	oxidized, CA 52.305, CB 39.556 ppm	oxidized, CA 52.335, CB 46.866 ppm	2.021
A:54:CYS:SG	A:59:CYS:SG	oxidized, CA 52.587, CB 43.282 ppm	oxidized, CA 53.694, CB 43.289 ppm	2.025

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

0--------10--------20--------30--------40--------50--------60
MLKCNKLVPIAYKTCPEGKNLCYKMFMMSDLTIPVKRGCIDVCPKNSLLVKYVCCNTDRCN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLKCNKLVPIAYKTCPEGKNLCYKMFMMSDLTIPVKRGCIDVCPKNSLLVKYVCCNTDRCN
--------10--------20--------30--------40--------50--------60-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0

Content subtype: combined_30172_5t8a.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	729		100.0 (chain: A, length: 61)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	882 (1)	noe	98.4 (chain: A, length: 61)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	12 (1)	undefined	13.1 (chain: A, length: 61)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	88 (1)	hbond	57.4 (chain: A, length: 61)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	Warning	184 (182)	.	100.0 (chain: A, length: 61)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 383
  - ¹³C chemical shifts: 285
  - ¹⁵N chemical shifts: 61
- 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)
11	TYR	CG	125.87
11	TYR	CZ	155.03
22	TYR	CG	126.29
22	TYR	CZ	155.56
25	PHE	CG	136.2
51	TYR	CG	128.98
51	TYR	CZ	154.61

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	384	383	99.7
¹³C chemical shifts	283	278	98.2
¹⁵N chemical shifts	64	61	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	119	99.2
¹³C chemical shifts	122	117	95.9
¹⁵N chemical shifts	57	56	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	264	264	100.0
¹³C chemical shifts	161	161	100.0
¹⁵N chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0
¹³C chemical shifts	36	36	100.0

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of restraints: 881
- Weight of restraints: 1.0 (881)
- Potential type of restraints: upper-bound-parabolic (881)
- Range of distance target values: 2.4, 8.65 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 13.1%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: upper-bound-parabolic (12)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 57.4%
    - Total number of restraints: 88
    - Weight of restraints: 1.0 (88)
    - Potential type of restraints: upper-bound-parabolic (88)
    - Range of distance target values: 2.2, 3.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 100.0%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Structure from MOLMOL, all-beta sheet protein, cytolytic peptide, recombinant production, toxin

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Found 1 Document (0.789 seconds)

BMRB: 30172

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Cytotoxin 1, : 1 : 1 : 6 : 193 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail