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Found 1 Document (0.677 seconds)

BMRB: 25487

2MZG

Purotoxin-2 NMR structure in DPC micelles

Authors

Nadezhdin, K., Oparin, P., Vassilevski, A., Grishin, E., Arseniev, A.

Assembly

Purotoxin-2 in DPC micelles

Entity

1. Purotoxin-2 in DPC micelles (polymer, Thiol state: all disulfide bound), 64 monomers, 7264.279 Da Detail

AKACTPLLHD CSHDRHSCCR GDMFKYVCDC FYPEGEDKTE VCSCQQPKSH KIAEKIIDKA KTTL

Formula weight

7264.279 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS19:SG
2	disulfide	sing	1:CYS11:SG	1:CYS28:SG
3	disulfide	sing	1:CYS18:SG	1:CYS44:SG
4	disulfide	sing	1:CYS30:SG	1:CYS42:SG

Source organism

Alopecosa

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.3 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.3 % (607 of 729)	95.3 % (364 of 382)	63.7 % (181 of 284)	98.4 % (62 of 63)
Backbone	80.7 % (305 of 378)	96.1 % (122 of 127)	64.7 % (123 of 190)	98.4 % (60 of 61)
Sidechain	87.9 % (363 of 413)	94.9 % (242 of 255)	76.3 % (119 of 156)	100.0 % (2 of 2)
Aromatic	75.0 % (39 of 52)	96.2 % (25 of 26)	53.8 % (14 of 26)
Methyl	95.8 % (46 of 48)	95.8 % (23 of 24)	95.8 % (23 of 24)

1. entity

AKACTPLLHD CSHDRHSCCR GDMFKYVCDC FYPEGEDKTE VCSCQQPKSH KIAEKIIDKA KTTL

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 15N]	1 mM
2	DPC	natural abundance	100 mM
3	D2O	natural abundance	5 %
4	H2O	natural abundance	95 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.7 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.7 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2016-04-11

Citation

Structure of purotoxin-2 from wolf spider: modular design and membrane-assisted mode of action in arachnid toxins
Oparin, P.B., Nadezhdin, K.D., Berkut, A.A., Arseniev, A.S., Grishin, E.V., Vassilevski, A.A.
Biochem. J. (2016), 473, 3113-3126, PubMed 27412961 , DOI 10.1042/BCJ20160573 , Abstract

Related entities 1. Purotoxin-2 in DPC micelles, : 1 : 3 : 99 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25487_2mzg.nef
Input source #2: Coordindates	2mzg.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:4:CYS:SG	A:19:CYS:SG	oxidized, CA 51.793, CB 41.294 ppm	oxidized, CA 52.548, CB 39.39 ppm	1.874
A:11:CYS:SG	A:28:CYS:SG	oxidized, CA 52.756, CB 42.236 ppm	oxidized, CA 52.2, CB 37.787 ppm	1.987
A:18:CYS:SG	A:44:CYS:SG	oxidized, CA 54.574, CB 36.825 ppm	oxidized, CA 53.028, CB 36.825 ppm	1.984
A:30:CYS:SG	A:42:CYS:SG	oxidized, CA 52.389, CB 43.933 ppm	oxidized, CA 51.844, CB 46.48 ppm	2.003

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--------40--------50--------60----
AKACTPLLHDCSHDRHSCCRGDMFKYVCDCFYPEGEDKTEVCSCQQPKSHKIAEKIIDKAKTTL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AKACTPLLHDCSHDRHSCCRGDMFKYVCDCFYPEGEDKTEVCSCQQPKSHKIAEKIIDKAKTTL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	64	0	0	100.0

Content subtype: combined_25487_2mzg.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_chem_shift_list_1	Warning	607		100.0 (chain: A, length: 64)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	571 (1)	noe	100.0 (chain: A, length: 64)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 369
  - ¹³C chemical shifts: 176
  - ¹⁵N chemical shifts: 62
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	369	96.6
¹³C chemical shifts	284	176	62.0
¹⁵N chemical shifts	65	62	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	127	126	99.2
¹³C chemical shifts	128	57	44.5
¹⁵N chemical shifts	61	60	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	255	243	95.3
¹³C chemical shifts	156	119	76.3
¹⁵N chemical shifts	4	2	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	23	92.0
¹³C chemical shifts	25	23	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	25	96.2
¹³C chemical shifts	26	14	53.8

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: 64, Sequence coverage: 100.0%
- Total number of restraints: 571
- Weight of restraints: 1.0 (571)
- Potential type of restraints: upper-bound-parabolic (571)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords DPC micelles, NMR structure, module toxin, purotoxin-2, spider venom

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Found 1 Document (0.677 seconds)

BMRB: 25487

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Purotoxin-2 in DPC micelles, : 1 : 3 : 99 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail