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BMRB: 18722

2LYE

High resolution NMR solution structure of a symmetrical theta-defensin, BTD-2.

Authors

Conibear, A.C., Rosengren, K., Harvey, P.J., Craik, D.J.

Assembly

BTD-2

Entity

1. BTD-2 (polymer, Thiol state: all disulfide bound), 18 monomers, 2084.613 Da Detail

GVCRCVCRRG VCRCVCRR

Formula weight

2084.613 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS16:SG
2	disulfide	sing	1:CYS5:SG	1:CYS14:SG
3	disulfide	sing	1:CYS7:SG	1:CYS12: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: 100.0 %, Completeness: 86.6 %, Completeness (bb): 81.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.6 % (168 of 194)	94.2 % (98 of 104)	75.0 % (54 of 72)	88.9 % (16 of 18)
Backbone	81.5 % (88 of 108)	100.0 % (38 of 38)	65.4 % (34 of 52)	88.9 % (16 of 18)
Sidechain	94.1 % (96 of 102)	90.9 % (60 of 66)	100.0 % (36 of 36)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. BTD-2

GVCRCVCRRG VCRCVCRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 0.8 mM, pH 6

#	Name	Isotope labeling	Concentration
1	BTD-2	natural abundance	0.8 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 0.9 mM, pH 6

#	Name	Isotope labeling	Type	Concentration
4	BTD-2	natural abundance		0.9 mM
5	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2012-11-26

Citation

Structural characterization of the cyclic cystine ladder motif of θ-defensins
Conibear, A.C., Rosengren, K., Harvey, P.J., Craik, D.J.
Biochemistry (2012), 51, 9718-9726, PubMed 23148585 , DOI 10.1021/bi301363a , Abstract

Related entities 1. BTD-2, : 1 : 1 : 3 : 9 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18722_2lye.nef
Input source #2: Coordindates	2lye.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	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:3:CYS:SG	A:16:CYS:SG	oxidized, CA 55.354, CB 47.049 ppm	oxidized, CA 55.286, CB 48.201 ppm	2.036
A:5:CYS:SG	A:14:CYS:SG	oxidized, CA 55.556, CB 48.567 ppm	oxidized, CA 55.556, CB 48.567 ppm	2.034
A:7:CYS:SG	A:12:CYS:SG	oxidized, CA 55.286, CB 48.201 ppm	oxidized, CA 55.354, CB 47.049 ppm	2.038

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--------
GVCRCVCRRGVCRCVCRR
||||||||||||||||||
GVCRCVCRRGVCRCVCRR

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_18722_2lye.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	168		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	95 (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	42 (42)	.	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: 98
  - ¹³C chemical shifts: 54
  - ¹⁵N chemical shifts: 16
- 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	104	97	93.3
¹³C chemical shifts	72	54	75.0
¹⁵N chemical shifts	24	16	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	37	97.4
¹³C chemical shifts	36	18	50.0
¹⁵N chemical shifts	18	16	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	60	90.9
¹³C chemical shifts	36	36	100.0
¹⁵N chemical shifts	6	0	0.0

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

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: 94
- Weight of restraints: 1.0 (94)
- Potential type of restraints: lower-bound-parabolic (1), square-well-parabolic (93)
- Range of distance target values: 2.0, 5.14 (Å)
- Histogram of 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: 42
- Total number of restraints per polymer type: 42
- Weight of restraints: 1.0 (42)
- Potential type of restraints: square-well-parabolic (42)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cyclic cystine ladder, cyclic peptides, theta-defensin

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Found 1 Document (0.37 seconds)

BMRB: 18722

Sample #1

Sample #2

Related entities 1. BTD-2, : 1 : 1 : 3 : 9 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail