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BMRB: 17681

2LDS

Solution Structure of a Short-chain LaIT1 from the Venom of Scorpion Liocheles australasiae

Authors

Horita, S., Miyakawa, T., Nagata, K., Tanokura, M.

Assembly

short chain LaIT 1

Entity

1. short chain LaIT 1 (polymer, Thiol state: all disulfide bound), 36 monomers, 4206.928 Da Detail

DFPLSKEYET CVRPRKCQPP LKCNKAQICV DPKKGW

Formula weight

4206.928 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS23:SG
2	disulfide	sing	1:CYS17:SG	1:CYS29:SG

Source organism

Liocheles australasiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 72.8 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.8 % (327 of 449)	78.6 % (191 of 243)	59.1 % (101 of 171)	100.0 % (35 of 35)
Backbone	81.6 % (168 of 206)	98.5 % (67 of 68)	65.4 % (70 of 107)	100.0 % (31 of 31)
Sidechain	69.8 % (194 of 278)	70.9 % (124 of 175)	66.7 % (66 of 99)	100.0 % (4 of 4)
Aromatic	43.3 % (13 of 30)	66.7 % (10 of 15)	14.3 % (2 of 14)	100.0 % (1 of 1)
Methyl	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)

1. entity

DFPLSKEYET CVRPRKCQPP LKCNKAQICV DPKKGW

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

Protein Blocks Logo

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

Release date

2011-08-24

Citation

Solution structure of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae
Horita, S., Matsushita, N., Kawachi, T., Ayabe, R., Miyashita, M., Miyakawa, T., Nakagawa, Y., Nagata, K., Miyagawa, H., Tanokura, M.
Biochem. Biophys. Res. Commun. (2011), 411, 738-744, PubMed 21782787 , DOI 10.1016/j.bbrc.2011.07.016 , Abstract

Related entities 1. short chain LaIT 1, : 1 : 1 : 5 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

3 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

8 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	MES	natural abundance		20 mM
4	sodium chloride	natural abundance		50 mM
5	LaIt_1	[U-13C; U-15N; U-1H]		1.5 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17681_2lds.nef
Input source #2: Coordindates	2lds.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:11:CYS:SG	A:23:CYS:SG	oxidized, CA 55.588, CB 44.094 ppm	oxidized, CB 40.073 ppm	2.051
A:17:CYS:SG	A:29:CYS:SG	oxidized, CA 54.273, CB 39.626 ppm	oxidized, CA 54.759, CB 40.213 ppm	1.917

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------
DFPLSKEYETCVRPRKCQPPLKCNKAQICVDPKKGW
||||||||||||||||||||||||||||||||||||
DFPLSKEYETCVRPRKCQPPLKCNKAQICVDPKKGW

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_17681_2lds.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	326		100.0 (chain: A, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	220 (1)	noe	91.7 (chain: A, length: 36)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	6 (1)	disulfide_bond	11.1 (chain: A, length: 36)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	6 (1)	disulfide_bond	11.1 (chain: A, length: 36)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	230 (1)	noe	88.9 (chain: A, length: 36)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	4 (1)	hbond	5.6 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_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: 191
  - ¹³C chemical shifts: 100
  - ¹⁵N chemical shifts: 35
- 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

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: 91.7%
- Total number of restraints: 220
- Weight of restraints: 1.0 (220)
- Potential type of restraints: upper-bound-parabolic (220)
- Range of distance target values: 3.1, 10.35 (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: disulfide_bond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 11.1%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - 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_6
    - Status: Warning
    - Experiment type: disulfide_bond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 11.1%
    - Total number of restraints: 6
    - Weight of restraints: 1.0 (6)
    - Potential type of restraints: upper-bound-parabolic (6)
    - Range of distance target values: 2.0, 3.0 (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: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 88.9%
        --------10--------20--------30------ DFPLSKEYETCVRPRKCQPPLKCNKAQICVDPKKGW ||||||||||| ||||||||||| ||||||||| | .FPLSKEYETCV.PRKCQPPLKCN.AQICVDPKK.W
      - Total number of restraints: 230
        Intra-residue restraints, i = j : 34
        Sequential restraints, | i - j | = 1 : 78
        Backbone-side chain: 50
        Side chain-side chain: 28
        Medium range restraints, 1 < | i - j | < 5 : 32
        Backbone-side chain: 14
        Side chain-side chain: 18
        Long range restraints, | i - j | >= 5 : 86
      - Weight of restraints: 1.0 (230)
        Intra-residue restraints, i = j : 1.0 (34)
        Sequential restraints, | i - j | = 1 : 1.0 (78)
        Backbone-side chain: 1.0 (50)
        Side chain-side chain: 1.0 (28)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (32)
        Backbone-side chain: 1.0 (14)
        Side chain-side chain: 1.0 (18)
        Long range restraints, | i - j | >= 5 : 1.0 (86)
      - Potential type of restraints: upper-bound-parabolic (230)
        Intra-residue restraints, i = j : upper-bound-parabolic (34)
        Sequential restraints, | i - j | = 1 : upper-bound-parabolic (78)
        Backbone-side chain: upper-bound-parabolic (50)
        Side chain-side chain: upper-bound-parabolic (28)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (32)
        Backbone-side chain: upper-bound-parabolic (14)
        Side chain-side chain: upper-bound-parabolic (18)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (86)
      - Range of distance target values: 3.01, 7.91 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 5.6%
        Total number of restraints: 4
        Total hydrogen bond restraints: 4
        Weight of restraints: 1.0 (4)
        Total hydrogen bond restraints: 1.0 (4)
        Potential type of restraints: upper-bound-parabolic (4)
        Total hydrogen bond restraints: upper-bound-parabolic (4)
        Range of distance target values: 2.5, 3.5 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Keywords Inhibitor Cystine Knot (ICK) fold, scorpion toxin