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Found 1 Document (0.401 seconds)

BMRB: 18937

2M2X

[Aba3,5,7,12,14,16]BTD-2

Authors

Conibear, A.C., Rosengren, K., Daly, N.L., Troiera Henriques, S., Craik, D.J.

Assembly

[Aba3,5,7,12,14,16]BTD-2

Entity

1. [Aba3,5,7,12,14,16]BTD-2 (polymer, Thiol state: not present), 18 monomers, 1976.385 × 2 Da Detail

GVXRXVXRRG VXRXVXRR

Total weight

3952.77 Da

Max. entity weight

1976.385 Da

Source organism

Papio anubis

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 66.7 %, Completeness: 92.5 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	92.5 % (124 of 134)	100.0 % (80 of 80)	81.5 % (44 of 54)
Backbone	83.3 % (50 of 60)	100.0 % (26 of 26)	70.6 % (24 of 34)
Sidechain	100.0 % (84 of 84)	100.0 % (54 of 54)	100.0 % (30 of 30)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. [Aba3,5,7,12,14,16]BTD-2

GVXRXVXRRG VXRXVXRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 0.4 mM, pH 5

#	Name	Isotope labeling	Concentration
1	[Aba3,5,7,12,14,16]BTD-2	natural abundance	0.4 mM
2	DSS	natural abundance	10 ug
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 0.5 mM, pH 4

#	Name	Isotope labeling	Concentration
5	[Aba3,5,7,12,14,16]BTD-2	natural abundance	0.5 mM
6	DSS	natural abundance	10 ug
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M2X, Strand ID: A Detail

Release date

2013-02-26

Citation

The cyclic cystine ladder in θ-defensins is important for structure and stability, but not antibacterial activity
Conibear, A.C., Rosengren, K., Daly, N.L., Henriques, S., Craik, D.J.
J. Biol. Chem. (2013), 288, 10830-10840, PubMed 23430740 , DOI 10.1074/jbc.M113.451047 , Abstract

Entries sharing articles BMRB: 5 entries Detail

  BMRB: 18875 released on 2013-02-26
    Title [Aba5,14]BTD-2
  BMRB: 18913 released on 2013-02-26
    Title [Aba3,16]BTD-2
  BMRB: 18914 released on 2013-02-26
    Title [Aba3,7,12,16]BTD-2
  BMRB: 18931 released on 2013-02-26
    Title [Aba5,7,12,14]BTD-2
  BMRB: 18938 released on 2013-02-26
    Title BTD-2[3,4]

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18937_2m2x.nef
Input source #2: Coordindates	2m2x.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	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	True (see coordinates for details)
Overall data processing status	Warning

Disulfide bonds

None

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)
1:2:VAL:C	1:3:ABA:N	unknown	unknown	n/a
1:3:ABA:C	1:4:ARG:N	unknown	unknown	n/a
1:4:ARG:C	1:5:ABA:N	unknown	unknown	n/a
1:5:ABA:C	1:6:VAL:N	unknown	unknown	n/a
1:6:VAL:C	1:7:ABA:N	unknown	unknown	n/a
1:7:ABA:C	1:8:ARG:N	unknown	unknown	n/a
1:11:VAL:C	1:12:ABA:N	unknown	unknown	n/a
1:12:ABA:C	1:13:ARG:N	unknown	unknown	n/a
1:13:ARG:C	1:14:ABA:N	unknown	unknown	n/a
1:14:ABA:C	1:15:VAL:N	unknown	unknown	n/a
1:15:VAL:C	1:16:ABA:N	unknown	unknown	n/a
1:16:ABA:C	1:17:ARG:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	5	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	7	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	12	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	14	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	16	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------
GVXRXVXRRGVXRXVXRR
||||||||||||||||||
GVXRXVXRRGVXRXVXRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0

Content subtype: combined_18937_2m2x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	13		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	164		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	126 (1)	noe	100.0 (chain: A, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	25 (25)	.	88.9 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 110
  - ¹³C chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	110	109	99.1
¹³C chemical shifts	72	54	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	37	97.4
¹³C chemical shifts	30	18	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	72	100.0
¹³C chemical shifts	42	36	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	14	8	57.1

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: 18, Sequence coverage: 100.0%
- Total number of restraints: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Range of distance target values: 2.06, 4.7 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 88.9%
- Total number of restraints: 25
- Total number of restraints per polymer type: 25
- Weight of restraints: 1.0 (25)
- Potential type of restraints: square-well-parabolic (25)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, cyclic cystine ladder, cyclic peptides, disulfide bond, theta-defensin

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Found 1 Document (0.401 seconds)

BMRB: 18937

Sample #1

Sample #2

Entries sharing articles BMRB: 5 entries Detail

Experiments performed 5 experiments Detail

Instrument

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Instrument

Sample

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Instrument

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NMR combined restraints 4 contents Detail