BMRBj - BMREntryMaster

Found 1 Document (0.516 seconds)

BMRB: 25758

2N6B

NMR structure of the de-novo toxin Hui1

Authors

Mendelman, N., Zhao, R., Goldstein, S.A.N., Chill, J.H.

Assembly

de-novo toxin Hui1

Entity

1. de-novo toxin Hui1 (polymer), 34 monomers, 3980.725 Da Detail

ACKDYLPKSE CTQFRCRTSM KYRLNLCKKT CGTC

Formula weight

3980.725 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 63.1 %, Completeness (bb): 71.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	63.1 % (255 of 404)	80.0 % (172 of 215)	33.1 % (51 of 154)	91.4 % (32 of 35)
Backbone	71.8 % (145 of 202)	91.2 % (62 of 68)	50.5 % (51 of 101)	97.0 % (32 of 33)
Sidechain	53.6 % (126 of 235)	74.8 % (110 of 147)	18.6 % (16 of 86)	0.0 % (0 of 2)
Aromatic	23.1 % (6 of 26)	46.2 % (6 of 13)	0.0 % (0 of 13)
Methyl	40.9 % (9 of 22)	81.8 % (9 of 11)	0.0 % (0 of 11)

1. Hui1

ACKDYLPKSE CTQFRCRTSM KYRLNLCKKT CGTC

Show sample condition

Sample #1

Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	10 mM
3	D2O	natural abundance	7 %
4	H2O	natural abundance	93 %
5	Hui1	natural abundance	0.6 mM
6	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	natural abundance	99.9 %
11	Hui1	natural abundance	0.6 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2N6B, Strand ID: A Detail

Release date

2015-12-13

Citation

Designer and natural peptide toxin blockers of the KcsA potassium channel identified by phage display
Mendelman, N., Zhao, R., Cuello, L., Chill, J.H., Goldstein, S.
Proc. Natl. Acad. Sci. U. S. A. (2015), 112, E7013-E7021, PubMed 26627718 , DOI 10.1073/pnas.1514728112 , Abstract

Related entities 1. de-novo toxin Hui1, : 1 : 33 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	10 mM
3	D2O	natural abundance	7 %
4	H2O	natural abundance	93 %
5	Hui1	natural abundance	0.6 mM
6	sodium azide	natural abundance	0.02 %

2 2D_1H-NOESY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	10 mM
3	D2O	natural abundance	7 %
4	H2O	natural abundance	93 %
5	Hui1	natural abundance	0.6 mM
6	sodium azide	natural abundance	0.02 %

3 2D_1H-15N HSQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	10 mM
3	D2O	natural abundance	7 %
4	H2O	natural abundance	93 %
5	Hui1	natural abundance	0.6 mM
6	sodium azide	natural abundance	0.02 %

4 2D_1H-13C-HMQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	10 mM
3	D2O	natural abundance	7 %
4	H2O	natural abundance	93 %
5	Hui1	natural abundance	0.6 mM
6	sodium azide	natural abundance	0.02 %

5 2D 1H-1H TOCSY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	natural abundance	99.9 %
11	Hui1	natural abundance	0.6 mM

6 2D_1H-NOESY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	natural abundance	99.9 %
11	Hui1	natural abundance	0.6 mM

7 2D_1H-15N HSQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	natural abundance	99.9 %
11	Hui1	natural abundance	0.6 mM

8 2D_1H-13C-HMQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details 20mM phosphate buffer, 10mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	natural abundance	99.9 %
11	Hui1	natural abundance	0.6 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25758_2n6b.nef
Input source #2: Coordindates	2n6b.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:35:CYS:SG	unknown, CA 55.0 ppm	unknown, CA 56.2 ppm	2.032
A:12:CYS:SG	A:28:CYS:SG	oxidized, CA 52.0, CB 37.5 ppm	unknown, CA 53.6 ppm	2.026
A:17:CYS:SG	A:32:CYS:SG	oxidized, CA 56.5, CB 35.9 ppm	oxidized, CA 52.7, CB 35.5 ppm	2.03

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-----
ACKDYLPKSECTQFRCRTSMKYRLNLCKKTCGTC
||||||||||||||||||||||||||||||||||
ACKDYLPKSECTQFRCRTSMKYRLNLCKKTCGTC
--------10--------20--------30----

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_25758_2n6b.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	267		97.1 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	360 (1)	noe	97.1 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	65 (65)	.	94.1 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 187
  - ¹³C chemical shifts: 49
  - ¹⁵N chemical shifts: 31
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	179	83.3
¹³C chemical shifts	154	49	31.8
¹⁵N chemical shifts	38	31	81.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	64	94.1
¹³C chemical shifts	68	33	48.5
¹⁵N chemical shifts	33	31	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	115	78.2
¹³C chemical shifts	86	16	18.6
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	10	83.3
¹³C chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	6	46.2
¹³C chemical shifts	13	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of restraints: 359
- Weight of restraints: 1.0 (359)
- Potential type of restraints: square-well-parabolic (359)
- Range of distance target values: 2.2, 3.96 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 94.1%
- Total number of restraints: 65
- Total number of restraints per polymer type: 65
- Weight of restraints: 1.0 (65)
- Potential type of restraints: square-well-parabolic (65)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ShK, potassium channel, toxin

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.516 seconds)

BMRB: 25758

Sample #1

Sample #2

Related entities 1. de-novo toxin Hui1, : 1 : 33 entities Detail

Experiments performed 8 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail