BMRBj - BMREntryMaster

Found 1 Document (0.472 seconds)

BMRB: 25409

2MXH

NMR resolved structure of VG16KRKP, an antimicrobial peptide in SDS

Authors

Bhunia, A., Datta, A.

Assembly

VG16KRKP, an antimicrobial peptide in SDS

Entity

1. VG16KRKP, an antimicrobial peptide in SDS (polymer, Thiol state: all free), 16 monomers, 1760.116 Da Detail

VARGWKRKCP LFGKGG

Formula weight

1760.116 Da

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 79.0 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	79.0 % (83 of 105)	79.0 % (83 of 105)
Backbone	91.4 % (32 of 35)	91.4 % (32 of 35)
Sidechain	72.9 % (51 of 70)	72.9 % (51 of 70)
Aromatic	36.4 % (4 of 11)	36.4 % (4 of 11)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. antimicrobial peptide

VARGWKRKCP LFGKGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	antimicrobial peptide	natural abundance	0.5 mM
2	H2O	natural abundance	90 %
3	SDS	natural abundance	200 mM
4	D2O	natural abundance	10 %

Protein Blocks Logo

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

Release date

2015-02-01

Citation

De-novo design of antimicrobial peptides:insights into membrane permeabilisation, lipopolysachharide fragmentation and application in plant disease control
Bhunia, A., Datta, A.
Not known

Related entities 1. VG16KRKP, an antimicrobial peptide in SDS, : 1 : 9 : 3 : 106 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25409_2mxh.nef
Input source #2: Coordindates	2mxh.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------
VARGWKRKCPLFGKGG
||||||||||||||||
VARGWKRKCPLFGKGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	16	0	0	100.0

Content subtype: combined_25409_2mxh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	83		100.0 (chain: A, length: 16)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	143 (1)	noe	100.0 (chain: A, length: 16)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	26 (26)	.	100.0 (chain: A, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 83
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	83	79.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	32	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	51	72.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	4	36.4

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 143
- Weight of restraints: 1.0 (143)
- Potential type of restraints: upper-bound-parabolic (143)
- Range of distance target values: 3.3, 5.3 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 26
- Total number of restraints per polymer type: 26
- Weight of restraints: 1.0 (26)
- Potential type of restraints: square-well-parabolic (26)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords peptide, turn, short helical segment

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.472 seconds)

BMRB: 25409

Sample

Related entities 1. VG16KRKP, an antimicrobial peptide in SDS, : 1 : 9 : 3 : 106 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail