BMRBj - BMREntryMaster

Found 1 Document (0.494 seconds)

BMRB: 34348

6QEU

[1-40]Gga-AvBD11

Authors

Meudal, H., Loth, K., Delmas, A.F., Landon, C.

Assembly

Gallinacin-11

Entity

1. Gallinacin-11 (polymer, Thiol state: all disulfide bound), 40 monomers, 4526.297 Da Detail

LPRDTSRCVG YHGYCIRSKV CPKPFAAFGT CSWRQKTCCV

Formula weight

4526.297 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS8:SG	1:CYS38:SG
2	disulfide	sing	1:CYS15:SG	1:CYS31:SG
3	disulfide	sing	1:CYS21:SG	1:CYS39:SG
4	disulfide	sing	1:CYS31:SG	1:CYS38:SG

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 76.4 %, Completeness (bb): 79.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.4 % (352 of 461)	99.2 % (239 of 241)	43.6 % (79 of 181)	87.2 % (34 of 39)
Backbone	79.5 % (186 of 234)	98.8 % (79 of 80)	62.4 % (73 of 117)	91.9 % (34 of 37)
Sidechain	76.5 % (202 of 264)	99.4 % (160 of 161)	41.6 % (42 of 101)	0.0 % (0 of 2)
Aromatic	48.1 % (25 of 52)	96.2 % (25 of 26)	0.0 % (0 of 25)	0.0 % (0 of 1)
Methyl	70.0 % (21 of 30)	100.0 % (15 of 15)	40.0 % (6 of 15)

1. entity 1

LPRDTSRCVG YHGYCIRSKV CPKPFAAFGT CSWRQKTCCV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 1.25 mM [1-40]Gga-AvBD11, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	[1-40]Gga-AvBD11	natural abundance		1.25 mM

LACS Plot; CA

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

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6QES, Strand ID: A Detail

Release date

2019-12-10

Citation

Structure, function, and evolution of Gga-AvBD11, the archetype of the structural avian-double-β-defensin family
Guyot, N., Meudal, H., Trapp, S., Iochmann, S., Silvestre, A., Jousset, G., Labas, V., Reverdiau, P., Loth, K., Herve, V., Aucagne, V., Delmas, A.F., Rehault-Godbert, S., Landon, C.
Proc. Natl. Acad. Sci. U. S. A. (2020), 117, 337-345, PubMed 31871151 , DOI 10.1073/pnas.1912941117 , Abstract

Related entities 1. Gallinacin-11, : 1 : 2 : 11 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34348_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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:8:CYS:SG	1:38:CYS:SG	oxidized, CA 56.75, CB 38.533 ppm	oxidized, CA 52.383, CB 37.558 ppm	n/a
1:15:CYS:SG	1:31:CYS:SG	oxidized, CA 50.942, CB 38.471 ppm	oxidized, CB 45.239 ppm	n/a
1:21:CYS:SG	1:39:CYS:SG	oxidized, CA 51.728, CB 39.02 ppm	oxidized, CA 50.285, CB 38.674 ppm	n/a
1:31:CYS:SG	1:38:CYS:SG	oxidized, CB 45.239 ppm	oxidized, CA 52.383, CB 37.558 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34348_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	380		100.0 (chain: 1, length: 40)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 40, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 270
  - ¹³C chemical shifts: 76
  - ¹⁵N chemical shifts: 34
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	THR	HG1	6.639

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	241	239	99.2
¹³C chemical shifts	181	76	42.0
¹⁵N chemical shifts	43	34	79.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	79	98.8
¹³C chemical shifts	80	36	45.0
¹⁵N chemical shifts	37	34	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	160	99.4
¹³C chemical shifts	101	40	39.6
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	4	26.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	25	96.2
¹³C chemical shifts	25	0	0.0
¹⁵N chemical shifts	1	0	0.0

Keywords ANTIMICROBIAL PROTEIN, avian egg, defensin, double-beta-defensin, new fold

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 (0.494 seconds)

BMRB: 34348

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Gallinacin-11, : 1 : 2 : 11 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail