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Found 1 Document (0.379 seconds)

BMRB: 19177

2M79

[Asp2,11]RTD-1

Authors

Conibear, A.C., Bochen, A., Rosengren, K., Kessler, H., Craik, D.J.

Assembly

[Asp2,11]RTD-1

Entity

1. [Asp2,11]RTD-1 (polymer, Thiol state: all disulfide bound), 18 monomers, 2089.499 Da Detail

GDCRCLCRRG DCRCICTR

Formula weight

2089.499 Da

Entity Connection

peptide 1, 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
4	peptide	sing	1:GLY1:N	1:ARG18:C

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: 86.5 %, Completeness (bb): 77.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	86.5 % (147 of 170)	95.0 % (96 of 101)	73.9 % (51 of 69)
Backbone	77.8 % (70 of 90)	94.7 % (36 of 38)	65.4 % (34 of 52)
Sidechain	96.9 % (93 of 96)	95.2 % (60 of 63)	100.0 % (33 of 33)
Methyl	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)

1. entity

GDCRCLCRRG DCRCICTR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3, Details 0.9 mM, pH 4

#	Name	Isotope labeling	Type	Concentration
1	[Asp2,11]RTD-1	natural abundance		0.9 mM
2	DSS	natural abundance		10 ug

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3, Details 0.5 mM, pH 3

#	Name	Isotope labeling	Type	Concentration
3	[Asp2,11]RTD-1	natural abundance		0.5 mM
4	DSS	natural abundance		10 ug

Protein Blocks Logo

Calculated from 20 models in PDB: 2M79, Strand ID: A Detail

Release date

2014-02-02

Citation

The cyclic cystine ladder of theta-defensins as a stable, bifunctional scaffold: A proof-of-concept study using the integrin-binding RGD motif
Conibear, A.C., Bochen, A., Rosengren, K., Stupar, P., Wang, C., Kessler, H., Craik, D.J.
Chembiochem. (2014), 15, 451-459, PubMed 24382674 , DOI 10.1002/cbic.201300568 , Abstract

Related entities 1. [Asp2,11]RTD-1, : 1 : 4 : 4 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_19177_2m79.nef
Input source #2: Coordindates	2m79.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 55.799, CB 46.371 ppm	oxidized, CA 55.542, CB 47.634 ppm	2.032
A:5:CYS:SG	A:14:CYS:SG	oxidized, CA 55.522, CB 47.261 ppm	oxidized, CA 55.681, CB 47.761 ppm	2.034
A:7:CYS:SG	A:12:CYS:SG	oxidized, CA 55.342, CB 47.558 ppm	oxidized, CA 55.664, CB 46.305 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--------
GDCRCLCRRGDCRCICTR
||||||||||||||||||
GDCRCLCRRGDCRCICTR

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_19177_2m79.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	152		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	116 (1)	noe	94.4 (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	40 (40)	.	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: 101
  - ¹³C chemical shifts: 51
- 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	101	100	99.0
¹³C chemical shifts	69	51	73.9

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	63	100.0
¹³C chemical shifts	33	33	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	5	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: 94.4%
- Total number of restraints: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: lower-bound-parabolic (1), square-well-parabolic (115)
- Range of distance target values: 2.05, 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: 40
- Total number of restraints per polymer type: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cyclic cystine ladder, cyclic peptides, integrin-binding, theta-defensin

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Found 1 Document (0.379 seconds)

BMRB: 19177

Sample #1

Sample #2

Related entities 1. [Asp2,11]RTD-1, : 1 : 4 : 4 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail