BMRBj - BMREntryMaster

Found 1 Document (0.625 seconds)

BMRB: 18043

2LLD

The Insect Defensin Lucifensin from Lucilia sericata

Authors

Nygaard, M.K.E., Andersen, A.S., Kristensen, H., Krogfelt, K.A., Fojan, P., Wimmer, R.

Assembly

Insect Defensin Lucifensin from Lucilia sericata

Entity

1. Insect Defensin Lucifensin from Lucilia sericata (polymer, Thiol state: all disulfide bound), 40 monomers, 4122.746 Da Detail

ATCDLLSGTG VKHSACAAHC LLRGNRGGYC NGRAICVCRN

Formula weight

4122.746 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS30:SG
2	disulfide	sing	1:CYS16:SG	1:CYS36:SG
3	disulfide	sing	1:CYS20:SG	1:CYS38:SG

Source organism

Lucilia sericata

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 80.0 %, Completeness (bb): 73.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	80.0 % (288 of 360)	93.7 % (193 of 206)	61.7 % (95 of 154)
Backbone	73.5 % (147 of 200)	93.0 % (80 of 86)	58.8 % (67 of 114)
Sidechain	89.2 % (173 of 194)	94.2 % (113 of 120)	81.1 % (60 of 74)
Aromatic	50.0 % (8 of 16)	100.0 % (8 of 8)	0.0 % (0 of 8)
Methyl	92.9 % (39 of 42)	100.0 % (21 of 21)	85.7 % (18 of 21)

1. lucifensin

ATCDLLSGTG VKHSACAAHC LLRGNRGGYC NGRAICVCRN

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LLD, Strand ID: A Detail

Release date

2012-03-06

Citation

The insect defensin lucifensin from Lucilia sericata
Nygaard, M.K.E., Andersen, A.S., Kristensen, H., Krogfelt, K.A., Fojan, P., Wimmer, R.
J. Biomol. NMR (2012), 52, 277-282, PubMed 22322867 , DOI 10.1007/s10858-012-9608-7 , Abstract

Related entities 1. Insect Defensin Lucifensin from Lucilia sericata, : 1 : 1 : 1 : 51 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

3 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

5 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.0, Details 2mM lucifensin in 10 mM K2HPO4 adjusted with 0.1 M NaOH to pH 5

#	Name	Isotope labeling	Type	Concentration
1	lucifensin	natural abundance		2 mM
2	potassium phosphate	natural abundance		10 mM
3	D2O	natural abundance		5 %
4	TSP	natural abundance		15 uM
5	H2O	natural abundance		95 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18043_2lld.nef
Input source #2: Coordindates	2lld.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	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)
A:3:CYS:SG	A:30:CYS:SG	oxidized, CB 41.532 ppm	oxidized, CA 55.09, CB 42.702 ppm	2.031
A:16:CYS:SG	A:36:CYS:SG	oxidized, CA 57.117, CB 35.801 ppm	oxidized, CB 35.763 ppm	2.027
A:20:CYS:SG	A:38:CYS:SG	unknown	oxidized, CA 52.075, CB 36.43 ppm	2.032

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

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40
ATCDLLSGTGVKHSACAAHCLLRGNRGGYCNGRAICVCRN
||||||||||||||||||||||||||||||||||||||||
ATCDLLSGTGVKHSACAAHCLLRGNRGGYCNGRAICVCRN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0

Content subtype: combined_18043_2lld.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	288		97.5 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	631 (1)	noe	100.0 (chain: A, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	83 (83)	.	100.0 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 97.5%
- Total number of assignments
  - ¹H chemical shifts: 196
  - ¹³C chemical shifts: 92
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
- Total number of restraints: 623
- Weight of restraints: 1.0 (623)
- Potential type of restraints: square-well-parabolic (623)
- Range of distance target values: 1.55, 4.83 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
- Total number of restraints: 83
- Total number of restraints per polymer type: 83
- Weight of restraints: 1.0 (83)
- Potential type of restraints: square-well-parabolic (83)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, insect defensin, lucifensin, Lucilia sericata, maggot debridement therapy