BMRBj - BMREntryMaster

Found 1 Document (0.636 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.636 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