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Found 1 Document (0.597 seconds)

BMRB: 25302

2MW7

Solution NMR structure of a novel cysteine framework containing Conus peptide Mo3964

Authors

Sarma, S.P., Kancherla, A.

Assembly

Monomer of Mo3964

Entity

1. Monomer of Mo3964 (polymer, Thiol state: all disulfide bound), 37 monomers, 3970.361 Da Detail

DGECGDKDEP CCGRPDGAKV CNDPWVCILT SSRCENP

Formula weight

3970.361 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS21:SG
2	disulfide	sing	1:CYS11:SG	1:CYS27:SG
3	disulfide	sing	1:CYS12:SG	1:CYS34:SG

Source organism

Conus monile

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.2 %, Completeness (bb): 99.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.2 % (374 of 381)	97.0 % (195 of 201)	100.0 % (144 of 144)	97.2 % (35 of 36)
Backbone	99.1 % (212 of 214)	98.6 % (73 of 74)	100.0 % (107 of 107)	97.0 % (32 of 33)
Sidechain	97.5 % (195 of 200)	96.1 % (122 of 127)	100.0 % (70 of 70)	100.0 % (3 of 3)
Aromatic	100.0 % (12 of 12)	100.0 % (6 of 6)	100.0 % (5 of 5)	100.0 % (1 of 1)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. Mo3964

DGECGDKDEP CCGRPDGAKV CNDPWVCILT SSRCENP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
6	Mo3964	[U-15N]	0.5 ~ 1.0 mM
7	sodium azide	natural abundance	0.02 %
8	sodium acetate	[U-100% 2H]	50 mM
9	H2O	natural abundance	90 %
10	D2O	[U-100% 2H]	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
11	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
12	sodium azide	natural abundance	0.02 %
13	sodium acetate	[U-100% 2H]	50 mM
14	D2O	[U-100% 2H]	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
15	Mo3964	[U-15N]	0.5 ~ 1.0 mM
16	sodium azide	natural abundance	0.02 %
17	sodium acetate	[U-100% 2H]	50 mM
18	D2O	[U-100% 2H]	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MW7, Strand ID: A Detail

Release date

2015-09-20

Citation

A Disulfide Stabilized β-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin
Kancherla, A.K., Meesala, S., Jorwal, P., Palanisamy, R., Sikdar, S.K., Sarma, S.P.
ACS Chem. Biol. (2015), 10, 1847-1860, PubMed 25961405 , DOI 10.1021/acschembio.5b00226 , Abstract

Related entities 1. Monomer of Mo3964, : 2 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

2 3D CBCA(CO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

3 3D HNCACB

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

4 3D HNCO

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

5 3D HN(CA)CO

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

6 3D C(CO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

7 3D H(CCO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

8 3D 1H-15N TOCSY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

9 3D 1H-15N NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

10 3D HCCH-COSY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

11 2D 1H-13C HSQC aromatic

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
11	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
12	sodium azide	natural abundance	0.02 %
13	sodium acetate	[U-100% 2H]	50 mM
14	D2O	[U-100% 2H]	100 %

12 3D HNHA

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

13 3D HCACO

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
11	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
12	sodium azide	natural abundance	0.02 %
13	sodium acetate	[U-100% 2H]	50 mM
14	D2O	[U-100% 2H]	100 %

14 3D 1H-13C NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
11	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
12	sodium azide	natural abundance	0.02 %
13	sodium acetate	[U-100% 2H]	50 mM
14	D2O	[U-100% 2H]	100 %

15 2D 1H-13C HSQC aliphatic

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
11	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
12	sodium azide	natural abundance	0.02 %
13	sodium acetate	[U-100% 2H]	50 mM
14	D2O	[U-100% 2H]	100 %

16 2D 1H-15N HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
6	Mo3964	[U-15N]	0.5 ~ 1.0 mM
7	sodium azide	natural abundance	0.02 %
8	sodium acetate	[U-100% 2H]	50 mM
9	H2O	natural abundance	90 %
10	D2O	[U-100% 2H]	10 %

17 2D 1H-15N HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05), Details pH was 5.35 without the isotope correction

#	Name	Isotope labeling	Concentration
15	Mo3964	[U-15N]	0.5 ~ 1.0 mM
16	sodium azide	natural abundance	0.02 %
17	sodium acetate	[U-100% 2H]	50 mM
18	D2O	[U-100% 2H]	100 %

18 3D HNHB

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
6	Mo3964	[U-15N]	0.5 ~ 1.0 mM
7	sodium azide	natural abundance	0.02 %
8	sodium acetate	[U-100% 2H]	50 mM
9	H2O	natural abundance	90 %
10	D2O	[U-100% 2H]	10 %

19 3D HN(CO)HB

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

20 3D HNCO_LRA

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.35 (±0.05)

#	Name	Isotope labeling	Concentration
1	Mo3964	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	sodium azide	natural abundance	0.02 %
3	sodium acetate	[U-100% 2H]	50 mM
4	H2O	natural abundance	90 %
5	D2O	[U-100% 2H]	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25302_2mw7.nef
Input source #2: Coordindates	2mw7.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:4:CYS:SG	A:12:CYS:SG	oxidized, CA 54.123, CB 46.59 ppm	oxidized, CA 53.235, CB 40.251 ppm	2.033
A:11:CYS:SG	A:27:CYS:SG	oxidized, CA 55.442, CB 40.671 ppm	oxidized, CA 56.656, CB 39.867 ppm	2.025
A:21:CYS:SG	A:34:CYS:SG	oxidized, CA 55.011, CB 46.324 ppm	oxidized, CA 53.695, CB 41.109 ppm	2.031

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--------30-------
DGECGDKDEPCCGRPDGAKVCNDPWVCILTSSRCENP
|||||||||||||||||||||||||||||||||||||
DGECGDKDEPCCGRPDGAKVCNDPWVCILTSSRCENP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0

Content subtype: combined_25302_2mw7.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_chem_shift_list_1	Warning	381		100.0 (chain: A, length: 37)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	600 (1)	noe	100.0 (chain: A, length: 37)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	86 (86)	.	100.0 (chain: A, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 200
  - ¹³C chemical shifts: 144
  - 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)
14	ARG	HH11	7.361
14	ARG	HH12	7.505
14	ARG	HH21	6.751
14	ARG	HH22	6.602
14	ARG	NH1	84.127
14	ARG	NH2	71.603
33	ARG	HH11	7.029
33	ARG	HH12	6.884
33	ARG	NH1	84.509

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	194	96.5
¹³C chemical shifts	144	144	100.0
¹⁵N chemical shifts	38	34	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	72	97.3
¹³C chemical shifts	74	74	100.0
¹⁵N chemical shifts	33	31	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	127	122	96.1
¹³C chemical shifts	70	70	100.0
¹⁵N chemical shifts	5	3	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	5	5	100.0
¹⁵N chemical shifts	1	1	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: 37, Sequence coverage: 100.0%
- Total number of restraints: 599
- Weight of restraints: 1.0 (599)
- Potential type of restraints: upper-bound-parabolic (599)
- Range of distance target values: 2.5, 6.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 86
- Total number of restraints per polymer type: 86
- Weight of restraints: 1.0 (86)
- Potential type of restraints: square-well-parabolic (86)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Conotoxin, Disulfide bonds, ion-channel modulator

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Found 1 Document (0.597 seconds)

BMRB: 25302

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Sample #2

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Sample #4

Related entities 1. Monomer of Mo3964, : 2 entities Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 4 contents Detail