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BMRB: 25926

2NA3

NMR Structure of KR-12: A minimalized domain derived from the human cathelicidin LL-37

Authors

Gunasekera, S., Goransson, U.

Assembly

KR-12

Entity

1. KR-12 (polymer, Thiol state: not present), 12 monomers, 1571.910 Da Detail

KRIVQRIKDF LR

Formula weight

1571.91 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.5 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	91.5 % (86 of 94)	91.5 % (86 of 94)
Backbone	95.8 % (23 of 24)	95.8 % (23 of 24)
Sidechain	90.0 % (63 of 70)	90.0 % (63 of 70)
Aromatic	80.0 % (4 of 5)	80.0 % (4 of 5)
Methyl	87.5 % (7 of 8)	87.5 % (7 of 8)

1. entity

KRIVQRIKDF LR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microliters of H2O/D2O (9:1 v/v) at pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	KR-12	natural abundance		1 mM

Sample #2

Solvent system 100% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microleters of D2O at pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	D2O	natural abundance		100 %
5	KR-12	natural abundance		1 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 2NA3, Strand ID: A Detail

Release date

2016-01-04

Citation

Backbone-cyclized stable peptide-dimers derived from the human cathelicidin LL-37 mediate potent antimicrobial activity
Gunasekera, S., Muhammad, T., Stromstedt, A.A., Rosengren, K.J., Goransson, U.
Not known

Related entities 1. KR-12, : 1 : 18 : 4 : 1 entities Detail

Interaction partners 1. KR-12, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 7 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microliters of H2O/D2O (9:1 v/v) at pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	KR-12	natural abundance		1 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microliters of H2O/D2O (9:1 v/v) at pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	KR-12	natural abundance		1 mM

3 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microliters of H2O/D2O (9:1 v/v) at pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	KR-12	natural abundance		1 mM

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microliters of H2O/D2O (9:1 v/v) at pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		90 %
2	D2O	natural abundance		10 %
3	KR-12	natural abundance		1 mM

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microleters of D2O at pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	D2O	natural abundance		100 %
5	KR-12	natural abundance		1 mM

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microleters of D2O at pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	D2O	natural abundance		100 %
5	KR-12	natural abundance		1 mM

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz BRUKER Avance HDIII equipped with a 5 mm TCI cryo probe.

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 4.5, Details 1 mM peptide dissolved in 600 microleters of D2O at pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	D2O	natural abundance		100 %
5	KR-12	natural abundance		1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25926_2na3.nef
Input source #2: Coordindates	2na3.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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--
KRIVQRIKDFLR
||||||||||||
KRIVQRIKDFLR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0

Content subtype: combined_25926_2na3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	91		100.0 (chain: A, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	331 (1)	noe	100.0 (chain: A, length: 12)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	16 (1)	hbond	58.3 (chain: A, length: 12)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	16 (16)	.	100.0 (chain: A, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 91
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 331
- Weight of restraints: 1.0 (331)
- Potential type of restraints: upper-bound-parabolic (331)
- Range of distance target values: 2.69, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 58.3%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: upper-bound-parabolic (16)
  - Range of distance target values: 1.7, 3.2 (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: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 16
- Total number of restraints per polymer type: 16
- Weight of restraints: 1.0 (16)
- Potential type of restraints: square-well-parabolic (16)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial, backbone-cyclized, cathelicidin, helical, peptide