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Found 1 Document (0.399 seconds)

BMRB: 18914

2M2H

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

Authors

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

Assembly

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

Entity

1. [Aba3,7,12,16]BTD-2 (polymer, Thiol state: all disulfide bound), 18 monomers, 2012.461 × 5 Da Detail

GVXRCVXRRG VXRCVXRR

Total weight

10062.306 Da

Max. entity weight

2012.461 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS14:SG

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: 77.8 %, Completeness: 89.9 %, Completeness (bb): 81.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	89.9 % (133 of 148)	100.0 % (88 of 88)	75.0 % (45 of 60)
Backbone	81.4 % (57 of 70)	100.0 % (30 of 30)	67.5 % (27 of 40)
Sidechain	97.8 % (88 of 90)	100.0 % (58 of 58)	93.8 % (30 of 32)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

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

GVXRCVXRRG VXRCVXRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 0.6 mM, pH 5

#	Name	Isotope labeling	Concentration
1	[Aba3,7,12,16]BTD-2	natural abundance	0.6 mM
2	DSS	natural abundance	10 ug
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 0.7 mM, pH 4

#	Name	Isotope labeling	Concentration
5	[Aba3,7,12,16]BTD-2	natural abundance	0.7 mM
6	DSS	natural abundance	10 ug
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M2H, 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

Related entities 1. [Aba3,7,12,16]BTD-2, : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18914_2m2h.nef
Input source #2: Coordindates	2m2h.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	True (see coordinates for details)
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:5:CYS:SG	A:14:CYS:SG	oxidized, CA 55.473, CB 46.967 ppm	oxidized, CA 55.473, CB 46.967 ppm	2.039

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
1:6: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
1:15: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	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	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--------
GVXRCVXRRGVXRCVXRR
||||||||||||||||||
GVXRCVXRRGVXRCVXRR

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_18914_2m2h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	160		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	136 (1)	noe	100.0 (chain: A, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	16 (1)	hbond	44.4 (chain: A, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	34 (34)	.	100.0 (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: 108
  - ¹³C chemical shifts: 52
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	107	99.1
¹³C chemical shifts	72	52	72.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	37	97.4
¹³C chemical shifts	32	18	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0
¹³C chemical shifts	40	34	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0
¹³C chemical shifts	12	8	66.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 136
- Weight of restraints: 1.0 (136)
- Potential type of restraints: lower-bound-parabolic (1), square-well-parabolic (135)
- Range of distance target values: 2.0, 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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 44.4%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: square-well-parabolic (16)
  - Range of distance target values: 1.9, 2.4 (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: 18, Sequence coverage: 100.0%
- Total number of restraints: 34
- Total number of restraints per polymer type: 34
- Weight of restraints: 1.0 (34)
- Potential type of restraints: square-well-parabolic (34)
- 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 (0.399 seconds)

BMRB: 18914

Sample #1

Sample #2

Related entities 1. [Aba3,7,12,16]BTD-2, : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail