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Found 1 Document (0.568 seconds)

BMRB: 34346

6QBL

NMR Structure of Big-defensin 1 from oyster Crassostrea gigas

Authors

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

Assembly

Big defensin 1

Entity

1. Big defensin 1 (polymer, Thiol state: all disulfide bound), 93 monomers, 10698.87 Da Detail

XAQALLPIAS YAGLTVSAPV FAALVTVYGA YALYRYNIRR RENSYQRIRS DHDSHSCANN RGWCRPTCFS HEYTDWFNND VCGSYRCCRP GRX

Formula weight

10698.87 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS57:SG	1:CYS87:SG
2	disulfide	sing	1:CYS64:SG	1:CYS82:SG
3	disulfide	sing	1:CYS68:SG	1:CYS88:SG

Source organism

Crassostrea gigas

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 77.9 %, Completeness (bb): 82.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.9 % (806 of 1034)	99.6 % (532 of 534)	46.2 % (186 of 403)	90.7 % (88 of 97)
Backbone	82.9 % (446 of 538)	100.0 % (183 of 183)	65.7 % (176 of 268)	100.0 % (87 of 87)
Sidechain	76.1 % (443 of 582)	99.4 % (349 of 351)	42.1 % (93 of 221)	10.0 % (1 of 10)
Aromatic	48.5 % (63 of 130)	96.9 % (63 of 65)	0.0 % (0 of 63)	0.0 % (0 of 2)
Methyl	71.2 % (57 of 80)	100.0 % (40 of 40)	42.5 % (17 of 40)

1. entity 1

XAQALLPIAS YAGLTVSAPV FAALVTVYGA YALYRYNIRR RENSYQRIRS DHDSHSCANN RGWCRPTCFS HEYTDWFNND VCGSYRCCRP GRX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.6, Details 1.0 mM [1-93]Cg-BigDef1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	[1-93]Cg-BigDef1	natural abundance		1.0 mM

LACS Plot; CA

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

Referencing offset: 2.61 ppm, Outliers: 5 Detail

LACS Plot; CB

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

Referencing offset: 2.61 ppm, Outliers: 5 Detail

LACS Plot; HA

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

Referencing offset: 0.06 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2019-12-02

Citation

The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets
Loth, K., Vergnes, A., Barreto, C., Voisin, S.N., Meudal, H., Da Silva, J., Bressan, A., Belmadi, N., Bachere, E., Aucagne, V., Cazevielle, C., Marchandin, H., Rosa, R.D., Bulet, P., Touqui, L., Delmas, A.F., Destoumieux-Garzon, D.
MBio (2019), 10, e01821-19-e01821-19, PubMed 31641083 , DOI 10.1128/mBio.01821-19 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34345 released on 2019-12-02
Title NMR Structure of Big-defensin 1 [44-93] from oyster Crassostrea gigas

Related entities 1. Big defensin 1, : 1 : 5 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34346_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)
1:57:CYS:SG	1:87:CYS:SG	oxidized, CA 52.906, CB 48.517 ppm	oxidized, CA 51.791, CB 35.93 ppm	n/a
1:64:CYS:SG	1:82:CYS:SG	oxidized 98.9%, reduced 1.1%, CA 50.485, CB 34.704 ppm	unknown	n/a
1:68:CYS:SG	1:88:CYS:SG	reduced, CA 50.752, CB 31.566 ppm	oxidized, CA 51.224, CB 38.11 ppm	n/a

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	1	PCA	PYROGLUTAMIC ACID	Assigned chemical shifts
1	93	AAR	ARGININEAMIDE	Assigned chemical shifts

Content subtype: bmr34346_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	890		100.0 (chain: 1, length: 93)
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: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹⁵N chemical shifts: 90
  - ¹³C chemical shifts: 172
  - ¹H chemical shifts: 628
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID
93	AAR

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
52	HIS	HD1	8.554
55	HIS	HD1	8.221

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	109	89	81.7
¹³C chemical shifts	406	170	41.9
¹H chemical shifts	540	537	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	88	88	100.0
¹³C chemical shifts	183	86	47.0
¹H chemical shifts	185	184	99.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	21	1	4.8
¹³C chemical shifts	223	84	37.7
¹H chemical shifts	355	353	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	40	10	25.0
¹H chemical shifts	40	40	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	2	0	0.0
¹³C chemical shifts	63	0	0.0
¹H chemical shifts	65	63	96.9

Keywords ANTIMICROBIAL PROTEIN, Big-defensin, antimicrobial, marine, oyster, salt insensitive activity

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Found 1 Document (0.568 seconds)

BMRB: 34346

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Big defensin 1, : 1 : 5 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail