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BMRB: 19142

2M6J

Structure of a vertebrate toxin from the badge huntsman spider

Authors

Brust, A., Vetter, I., Mobli, M., King, G., Fry, B.

Assembly

vertebrate toxin from the badge huntsman spider

Entity

1. AbTx (polymer, Thiol state: all disulfide bound), 26 monomers, 2701.234 Da Detail

IKSCETFIVA CDGGKACREV KCKTIX

2. vertebrate toxin from the badge huntsman spider, entity CAM (non-polymer), 152.233 Da

Total weight

2853.4668 Da

Max. entity weight

2701.234 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS22:SG
2	disulfide	sing	1:CYS11:SG	1:CYS17:SG

Source organism

Neosparassus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 81.7 %, Completeness (bb): 67.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.7 % (228 of 279)	99.3 % (144 of 145)	60.6 % (66 of 109)	72.0 % (18 of 25)
Backbone	67.3 % (101 of 150)	98.1 % (51 of 52)	43.8 % (32 of 73)	72.0 % (18 of 25)
Sidechain	98.7 % (150 of 152)	100.0 % (93 of 93)	96.6 % (57 of 59)
Aromatic	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)
Methyl	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (14 of 14)

1. AbTx

IKSCETFIVA CDGGKACREV KCKTIX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	AbTx	natural abundance		1 mM
2	CAMPHOR	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M6J, Strand ID: A Detail

Release date

2014-04-06

Citation

Structure of a novel vertebrate toxin from the badge huntsman spider
Brust, A., Vetter, I., Mobli, M., King, G., Fry, B.
Not known

Related entities 1. AbTx, : 1 : 1 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19142_2m6j.nef
Input source #2: Coordindates	2m6j.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	True (see coodinates for details)
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:22:CYS:SG	oxidized, CB 42.045 ppm	oxidized, CB 39.67 ppm	2.029
A:11:CYS:SG	A:17:CYS:SG	oxidized, CB 42.835 ppm	oxidized, CB 40.951 ppm	2.1

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)
1:25:ILE:C	1:26:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	26	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20------
IKSCETFIVACDGGKACREVKCKTIX
||||||||||||||||||||||||||
IKSCETFIVACDGGKACREVKCKTIX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	26	0	0	100.0

Content subtype: combined_19142_2m6j.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	232		100.0 (chain: A, length: 26)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	472 (1)	noe	96.2 (chain: A, length: 26)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	10 (1)	hbond	23.1 (chain: A, length: 26)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	28 (28)	.	88.5 (chain: A, length: 26)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 149
  - ¹³C chemical shifts: 64
  - ¹⁵N chemical shifts: 19
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
15	LYS	HZ1	7.52
15	LYS	HZ2	7.52
15	LYS	HZ3	7.52

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	146	99.3
¹³C chemical shifts	109	64	58.7
¹⁵N chemical shifts	27	19	70.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	51	98.1
¹³C chemical shifts	50	7	14.0
¹⁵N chemical shifts	26	19	73.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	95	100.0
¹³C chemical shifts	59	57	96.6
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	14	14	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 96.2%
- Total number of restraints: 470
- Weight of restraints: 1.0 (470)
- Potential type of restraints: upper-bound-parabolic (470)
- Range of distance target values: 2.4, 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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 23.1%
  - Total number of restraints: 10
  - Weight of restraints: 1.0 (10)
  - Potential type of restraints: upper-bound-parabolic (10)
  - Range of distance target values: 2.2, 3.2 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 88.5%
- 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 spider, toxin, venom

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Found 1 Document (0.54 seconds)

BMRB: 19142

Sample

Related entities 1. AbTx, : 1 : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail