BMRBj - BMREntryMaster

Found 1 Document (0.365 seconds)

BMRB: 30617

6PI2

NMR Solution structure of native tachyplesin II peptide

Authors

Harvey, P.J., Troeira Henriques, S., Vernen, F.

Assembly

Tachyplesin II

Entity

1. Tachyplesin II (polymer, Thiol state: all disulfide bound), 18 monomers, 2266.766 Da Detail

RWCFRVCYRG ICYRKCRX

Formula weight

2266.766 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS16:SG
2	disulfide	sing	1:CYS7:SG	1:CYS12:SG

Source organism

Limulus polyphemus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 76.0 %, Completeness (bb): 77.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.0 % (171 of 225)	90.9 % (110 of 121)	53.5 % (46 of 86)	83.3 % (15 of 18)
Backbone	77.5 % (79 of 102)	94.3 % (33 of 35)	62.0 % (31 of 50)	88.2 % (15 of 17)
Sidechain	77.7 % (108 of 139)	89.5 % (77 of 86)	59.6 % (31 of 52)	0.0 % (0 of 1)
Aromatic	39.5 % (15 of 38)	78.9 % (15 of 19)	0.0 % (0 of 18)	0.0 % (0 of 1)
Methyl	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)

1. entity 1

RWCFRVCYRG ICYRKCRX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/mL tachyplesin II, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	tachyplesin II	natural abundance		1.0 mg/mL

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/mL tachyplesin II, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	tachyplesin II	natural abundance		1.0 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6PI2, Strand ID: A Detail

Release date

2019-08-01

Citation

Characterization of Tachyplesin Peptides and Their Cyclized Analogues to Improve Antimicrobial and Anticancer Properties
Vernen, F., Harvey, P.J., Dias, S.A., Veiga, A.S., Huang, Y.H., Craik, D.J., Lawrence, N., Troeira Henriques, S.
Int. J. Mol. Sci. (2019), 20, E4184-E4184, PubMed 31455019 , DOI 10.3390/ijms20174184 , Abstract

Related entities 1. Tachyplesin II, : 1 : 4 : 18 entities Detail

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30617_3.str
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	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:3:CYS:SG	1:16:CYS:SG	oxidized, CA 55.435, CB 48.396 ppm	oxidized, CA 55.232, CB 47.542 ppm	n/a
1:7:CYS:SG	1:12:CYS:SG	oxidized, CA 55.201, CB 48.619 ppm	oxidized, CA 55.136, CB 47.601 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30617_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	177		94.4 (chain: 1, length: 18)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 94.4%
- Total number of assignments
  - ¹H chemical shifts: 117
  - ¹³C chemical shifts: 46
  - ¹⁵N chemical shifts: 14
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	123	109	88.6
¹³C chemical shifts	86	46	53.5
¹⁵N chemical shifts	24	14	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	32	91.4
¹³C chemical shifts	34	15	44.1
¹⁵N chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	77	87.5
¹³C chemical shifts	52	31	59.6
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	15	78.9
¹³C chemical shifts	18	0	0.0
¹⁵N chemical shifts	1	0	0.0

Keywords ANTIMICROBIAL PROTEIN, defense peptide

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 (0.365 seconds)

BMRB: 30617

Sample #1

Sample #2

Related entities 1. Tachyplesin II, : 1 : 4 : 18 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail