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BMRB: 25491

2MZL

Structure of Conantokin Rl-B

Authors

Castellino, F., Yuan, Y., Kunda, S., Zajicek, J.

Assembly

Conantokin Rl-B

Entity

1. Conantokin Rl-B (polymer, Thiol state: not present), 19 monomers, 2376.293 Da Detail

GEXXLQXNQX XLIRXKSNX

Formula weight

2376.293 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 63.2 %, Completeness: 89.9 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (134 of 149)	90.1 % (73 of 81)	96.2 % (50 of 52)	68.8 % (11 of 16)
Backbone	91.7 % (66 of 72)	96.0 % (24 of 25)	97.1 % (34 of 35)	66.7 % (8 of 12)
Sidechain	89.8 % (79 of 88)	87.5 % (49 of 56)	96.4 % (27 of 28)	75.0 % (3 of 4)
Methyl	100.0 % (12 of 12)	100.0 % (6 of 6)	100.0 % (6 of 6)

1. Conantokin GNQO

GEXXLQXNQX XLIRXKSNX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MZL, Strand ID: A Detail

Release date

2015-06-14

Citation

Hydroxyproline-induced Helical Disruption in Conantokin Rl-B Affects Subunit-selective Antagonistic Activities toward Ion Channels of N-Methyl-d-aspartate Receptors
Castellino, F., Yuan, Y., Kunda, S., Zajicek, J.
J. Biol. Chem. (2015), 290, 18156-18172, PubMed 26048991 , DOI 10.1074/jbc.M115.650341 , Abstract

Experiments performed 5 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

2 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details CONANTOKIN GNQO 2.0 mM; HEPES 10 mM; Magnesium Chloride 40 mM

#	Name	Isotope labeling	Type	Concentration
1	Conantokin GNQO	natural abundance		2 mM
2	HEPES	[U-100% 2H]		10 mM
3	DSS	natural abundance		0.01 mg/mL
4	sodium chloride	natural abundance		10 mM
5	magnesium chloride	natural abundance		40 mM
6	D2O	[U-100% 2H]		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25491_2mzl.nef
Input source #2: Coordindates	2mzl.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
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

None

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)
1:2:GLU:C	1:3:CGU:N	unknown	unknown	n/a
1:3:CGU:C	1:4:CGU:N	unknown	unknown	n/a
1:4:CGU:C	1:5:LEU:N	unknown	unknown	n/a
1:6:GLN:C	1:7:CGU:N	unknown	unknown	n/a
1:7:CGU:C	1:8:ASN:N	unknown	unknown	n/a
1:9:GLN:C	1:10:HYP:N	unknown	unknown	n/a
1:10:HYP:C	1:11:CGU:N	unknown	unknown	n/a
1:11:CGU:C	1:12:LEU:N	unknown	unknown	n/a
1:14:ARG:C	1:15:CGU:N	unknown	unknown	n/a
1:15:CGU:C	1:16:LYS:N	unknown	unknown	n/a
1:18:ASN:C	1:19:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	4	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	7	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	10	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	11	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	15	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	19	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10---------
GEXXLQXNQXXLIRXKSNX
|||||||||||||||||||
GEXXLQXNQXXLIRXKSNX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_25491_2mzl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	11		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	200		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	177 (1)	noe	94.7 (chain: A, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	28 (28)	.	94.7 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 110
  - ¹³C chemical shifts: 73
  - ¹⁵N chemical shifts: 17
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

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: 19, Sequence coverage: 94.7%
- Total number of restraints: 177
- Weight of restraints: 1.0 (177)
- Potential type of restraints: square-well-parabolic (177)
- Range of distance target values: 2.4, 4.5 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 94.7%
- Total number of restraints: 28
- Total number of restraints per polymer type: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords peptide