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Found 1 Document (0.523 seconds)

BMRB: 34014

5LCS

NMR structure of Chicken AvBD7 defensin

Authors

Landon, C., Loth, K., Meudal, H.

Assembly

Gallinacin-7

Entity

1. Gallinacin-7 (polymer, Thiol state: all disulfide bound), 47 monomers, 5359.210 Da Detail

XPFIPRPIDT CRLRNGICFP GICRRPYYWI GTCNNGIGSC CARGWRS

Formula weight

5359.21 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS40:SG
2	disulfide	sing	1:CYS18:SG	1:CYS33:SG
3	disulfide	sing	1:CYS23:SG	1:CYS41:SG

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 84.0 %, Completeness (bb): 74.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.0 % (451 of 537)	95.1 % (270 of 284)	66.7 % (138 of 207)	93.5 % (43 of 46)
Backbone	74.8 % (199 of 266)	95.7 % (89 of 93)	53.8 % (71 of 132)	95.1 % (39 of 41)
Sidechain	91.3 % (284 of 311)	94.8 % (181 of 191)	86.1 % (99 of 115)	80.0 % (4 of 5)
Aromatic	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (28 of 28)	100.0 % (2 of 2)
Methyl	94.1 % (32 of 34)	100.0 % (17 of 17)	88.2 % (15 of 17)

1. entity 1

XPFIPRPIDT CRLRNGICFP GICRRPYYWI GTCNNGIGSC CARGWRS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 0.23 mM Chicken AvBD7, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chicken AvBD7	natural abundance		0.23 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5LCS, Strand ID: A Detail

Release date

2016-09-01

Citation

The Unusual Resistance of Avian Defensin AvBD7 to Proteolytic Enzymes Preserves Its Antibacterial Activity
Bailleul, G., Kravtzoff, A., Joulin-Giet, A., Lecaille, F., Labas, V., Meudal, H., Loth, K., Teixeira-Gomes, A.P., Gilbert, F.B., Coquet, L., Jouenne, T., Bromme, D., Schouler, C., Landon, C., Lalmanach, G., Lalmanach, A.C.
PLoS One (2016), 11, e0161573-e0161573, PubMed 27561012 , DOI 10.1371/journal.pone.0161573 , Abstract

Related entities 1. Gallinacin-7, : 1 : 6 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34014_5lcs.nef
Input source #2: Coordindates	5lcs.cif
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	True (see coodinates for details)
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)
A:11:CYS:SG	A:40:CYS:SG	unknown	unknown	2.039
A:18:CYS:SG	A:33:CYS:SG	oxidized, CA 51.783, CB 37.977 ppm	unknown, CA 54.044 ppm	2.032
A:23:CYS:SG	A:41:CYS:SG	oxidized, CA 50.918, CB 36.43 ppm	unknown, CA 49.756 ppm	2.027

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:1:PCA:C	1:2:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	PCA	PYROGLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40-------
XPFIPRPIDTCRLRNGICFPGICRRPYYWIGTCNNGIGSCCARGWRS
|||||||||||||||||||||||||||||||||||||||||||||||
XPFIPRPIDTCRLRNGICFPGICRRPYYWIGTCNNGIGSCCARGWRS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_34014_5lcs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	468		100.0 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1211 (1)	noe	100.0 (chain: A, length: 47)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	16 (1)	hbond	21.3 (chain: A, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	70 (70)	.	89.4 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 289
  - ¹³C chemical shifts: 136
  - ¹⁵N chemical shifts: 43
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
39	SER	HG	5.761

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	288	99.3
¹³C chemical shifts	210	136	64.8
¹⁵N chemical shifts	54	43	79.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	93	97.9
¹³C chemical shifts	93	35	37.6
¹⁵N chemical shifts	42	39	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	195	195	100.0
¹³C chemical shifts	117	101	86.3
¹⁵N chemical shifts	12	4	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	15	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0
¹³C chemical shifts	28	26	92.9
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of restraints: 1162
- Weight of restraints: 1.0 (1162)
- Potential type of restraints: square-well-parabolic (1162)
- Range of distance target values: 1.44, 4.59 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 21.3%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: square-well-parabolic (16)
  - Range of distance target values: 2.21, 3.22 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 89.4%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, avian defensin, immune system

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Found 1 Document (0.523 seconds)

BMRB: 34014

Sample

Related entities 1. Gallinacin-7, : 1 : 6 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail