BMRBj - BMREntryMaster

Found 1 Document (0.606 seconds)

BMRB: 34345

6QBL

NMR Structure of Big-defensin 1 [44-93] 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), 50 monomers, 6001.514 Da Detail

SYQRIRSDHD SHSCANNRGW CRPTCFSHEY TDWFNNDVCG SYRCCRPGRX

Formula weight

6001.514 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS14:SG	1:CYS44:SG
2	disulfide	sing	1:CYS21:SG	1:CYS39:SG
3	disulfide	sing	1:CYS25:SG	1:CYS45:SG

Source organism

Crassostrea gigas

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 80.9 %, Completeness (bb): 83.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.9 % (448 of 554)	99.7 % (290 of 291)	50.7 % (106 of 209)	96.3 % (52 of 54)
Backbone	83.4 % (242 of 290)	99.0 % (98 of 99)	68.1 % (98 of 144)	97.9 % (46 of 47)
Sidechain	81.3 % (252 of 310)	100.0 % (192 of 192)	48.6 % (54 of 111)	85.7 % (6 of 7)
Aromatic	57.5 % (46 of 80)	100.0 % (40 of 40)	13.2 % (5 of 38)	50.0 % (1 of 2)
Methyl	71.4 % (10 of 14)	100.0 % (7 of 7)	42.9 % (3 of 7)

1. entity 1

SYQRIRSDHD SHSCANNRGW CRPTCFSHEY TDWFNNDVCG SYRCCRPGRX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.6, Details 1.5 mM [44-93]Cg-BigDef1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	[44-93]Cg-BigDef1	natural abundance		1.5 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: 3.01 ppm, Outliers: 1 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: 3.01 ppm, Outliers: 1 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: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6QBK, 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: 34346 released on 2019-12-02
Title NMR Structure of Big-defensin 1 from oyster Crassostrea gigas

Related entities 1. Big defensin 1, : 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	bmr34345_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)
1:14:CYS:SG	1:44:CYS:SG	oxidized, CA 52.771, CB 48.457 ppm	oxidized, CA 52.024, CB 35.886 ppm	n/a
1:21:CYS:SG	1:39:CYS:SG	oxidized 98.5%, reduced 1.5%, CA 50.404, CB 34.543 ppm	oxidized 96.5%, reduced 3.5%, CA 49.378, CB 34.004 ppm	n/a
1:25:CYS:SG	1:45:CYS:SG	reduced, CA 49.983, CB 31.504 ppm	oxidized, CA 51.087, CB 38.095 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	50	AAR	ARGININEAMIDE	Assigned chemical shifts

Content subtype: bmr34345_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	464		100.0 (chain: 1, length: 50)
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: 50, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 313
  - ¹³C chemical shifts: 98
  - ¹⁵N chemical shifts: 53
- 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
50	AAR

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	291	290	99.7
¹³C chemical shifts	209	96	45.9
¹⁵N chemical shifts	61	52	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	98	99.0
¹³C chemical shifts	98	49	50.0
¹⁵N chemical shifts	47	46	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	192	100.0
¹³C chemical shifts	111	47	42.3
¹⁵N chemical shifts	14	6	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	1	14.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	40	100.0
¹³C chemical shifts	38	0	0.0
¹⁵N chemical shifts	2	1	50.0

Keywords ANTIMICROBIAL PROTEIN, Big-defensin, antimicrobial, marine, oyster

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Found 1 Document (0.606 seconds)

BMRB: 34345

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

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

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail