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BMRB: 30149

5L1C

Heteronuclear Solution Structure of Chlorotoxin

Authors

Mobli, M., Braga, C.B., Sharma, G.

Assembly

Chlorotoxin

Entity

1. Chlorotoxin (polymer), 36 monomers, 4004.755 Da Detail

MCMPCFTTDH QMARKCDDCC GGKGRGKCYG PQCLCR

Formula weight

4004.755 Da

Source organism

Leiurus quinquestriatus quinquestriatus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.7 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (377 of 390)	99.0 % (206 of 208)	93.8 % (137 of 146)	94.4 % (34 of 36)
Backbone	95.8 % (203 of 212)	97.3 % (73 of 75)	95.1 % (98 of 103)	94.1 % (32 of 34)
Sidechain	98.1 % (205 of 209)	100.0 % (133 of 133)	94.6 % (70 of 74)	100.0 % (2 of 2)
Aromatic	81.8 % (18 of 22)	100.0 % (11 of 11)	63.6 % (7 of 11)
Methyl	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)

1. entity 1

MCMPCFTTDH QMARKCDDCC GGKGRGKCYG PQCLCR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5L1C, Strand ID: A Detail

Release date

2016-11-10

Citation

Solution structure and dynamics of Chlorotoxin, a glioma specific scorpion toxin
Braga, C.B., Sharma, G., Jia, X., Ramanujam, V., Rittner, R., Mobli, M.

Related entities 1. Chlorotoxin, : 1 : 5 : 1 : 3 : 39 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

2 3D HNCO

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

3 3D HNCACB

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

4 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

5 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

8 3D H(CCO)NH

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

9 3D C(CO)NH

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 900 MHz EQUIPPED WITH CRYOPROBE

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±0) atm, Temperature 298 (±0.5) K, pH 5.8 (±0.2), Details 370 uM [U-13C; U-15N] Chlorotoxin, 20 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chlorotoxin	[U-13C; U-15N]		370 (±10.0) uM
2	D2O	natural abundance		5 (±1.0) %
3	sodium phosphate	natural abundance		20 (±1.0) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30149_5l1c.nef
Input source #2: Coordindates	5l1c.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:2:CYS:SG	A:19:CYS:SG	oxidized, CA 60.82, CB 43.568 ppm	oxidized, CA 61.187, CB 40.635 ppm	2.008
A:5:CYS:SG	A:28:CYS:SG	oxidized, CA 56.586, CB 47.366 ppm	oxidized, CA 55.135, CB 41.167 ppm	2.012
A:16:CYS:SG	A:33:CYS:SG	oxidized, CA 56.67, CB 35.721 ppm	oxidized, CA 56.245, CB 37.994 ppm	1.991
A:20:CYS:SG	A:35:CYS:SG	oxidized, CA 54.599, CB 38.849 ppm	oxidized, CA 52.184, CB 35.312 ppm	2.051

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------
MCMPCFTTDHQMARKCDDCCGGKGRGKCYGPQCLCR
||||||||||||||||||||||||||||||||||||
MCMPCFTTDHQMARKCDDCCGGKGRGKCYGPQCLCR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0

Content subtype: combined_30149_5l1c.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	379		100.0 (chain: A, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	710 (1)	noe	100.0 (chain: A, length: 36)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	24 (1)	undefined	22.2 (chain: A, length: 36)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	57 (57)	.	100.0 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 206
  - ¹³C chemical shifts: 136
  - ¹⁵N chemical shifts: 37
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of restraints: 708
- Weight of restraints: 1.0 (708)
- Potential type of restraints: upper-bound-parabolic (708)
- Range of distance target values: 2.35, 5.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 22.2%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: upper-bound-parabolic (24)
  - Range of distance target values: 2.01, 3.07 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of restraints: 57
- Total number of restraints per polymer type: 57
- Weight of restraints: 1.0 (57)
- Potential type of restraints: square-well-parabolic (57)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords peptide disulfide rich peptide, scorpion toxin, venom