BMRBj - BMREntryMaster

Found 1 Document (0.499 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

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Found 1 Document (0.499 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