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Found 1 Document (0.586 seconds)

BMRB: 18723

2LYF

High resolution NMR solution structure of the theta-defensin RTD-1

Authors

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

Assembly

RTD-1

Entity

1. RTD-1 (polymer, Thiol state: all disulfide bound), 18 monomers, 2105.628 Da Detail

GFCRCLCRRG VCRCICTR

Formula weight

2105.628 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

Macaca mulatta

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.7 %, Completeness (bb): 77.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.7 % (140 of 201)	81.3 % (87 of 107)	53.9 % (41 of 76)	66.7 % (12 of 18)
Backbone	77.8 % (84 of 108)	100.0 % (38 of 38)	65.4 % (34 of 52)	66.7 % (12 of 18)
Sidechain	66.1 % (72 of 109)	71.0 % (49 of 69)	57.5 % (23 of 40)
Aromatic	0.0 % (0 of 10)	0.0 % (0 of 5)	0.0 % (0 of 5)
Methyl	57.1 % (8 of 14)	100.0 % (7 of 7)	14.3 % (1 of 7)

1. RTD-1

GFCRCLCRRG VCRCICTR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.0 (±1.0), Details 1.0 mM, pH 5

#	Name	Isotope labeling	Concentration
1	RTD-1	natural abundance	1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.0 (±1.0), Details 1.0 mM, pH 3

#	Name	Isotope labeling	Type	Concentration
4	RTD-1	natural abundance		1.0 mM
5	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LYF, 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. RTD-1, : 1 : 1 : 3 : 10 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_18723_2lyf.nef
Input source #2: Coordindates	2lyf.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 55.415, CB 47.259 ppm	oxidized, CA 55.471, CB 47.821 ppm	2.041
A:5:CYS:SG	A:14:CYS:SG	oxidized, CA 55.359, CB 48.035 ppm	oxidized, CA 55.606, CB 48.219 ppm	2.038
A:7:CYS:SG	A:12:CYS:SG	oxidized, CA 55.437, CB 48.035 ppm	oxidized, CA 55.302, CB 48.215 ppm	2.037

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--------
GFCRCLCRRGVCRCICTR
||||||||||||||||||
GFCRCLCRRGVCRCICTR

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_18723_2lyf.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	140		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	132 (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	38 (38)	.	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: 87
  - ¹³C chemical shifts: 41
  - ¹⁵N chemical shifts: 12
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	107	86	80.4
¹³C chemical shifts	76	41	53.9
¹⁵N chemical shifts	23	12	52.2

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	12	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	49	71.0
¹³C chemical shifts	40	23	57.5
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	1	14.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	0	0.0
¹³C chemical shifts	5	0	0.0

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: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Range of distance target values: 2.12, 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: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- 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 (0.586 seconds)

BMRB: 18723

Sample #1

Sample #2

Related entities 1. RTD-1, : 1 : 1 : 3 : 10 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