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BMRB: 30499

6E5K

Heterogeneous-Backbone Mimics of a Designed Disulfide-Rich Protein: Aib turn, Aib helix, N-methyl hairpin

Authors

Cabalteja, C.C., Mihalko, D.S., Horne, W.S.

Assembly

Designed peptide NC HEE D1: Aib turn, Aib helix, N-methyl hairpin mutant

Entity

1. Designed peptide NC HEE D1: Aib turn, Aib helix, N-methyl hairpin mutant (polymer, Thiol state: all disulfide bound), 28 monomers, 3150.660 Da Detail

NDXCKXLKXR YXGCEXRCDX PRYEXHCX

Formula weight

3150.66 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS18:SG
2	disulfide	sing	1:CYS14:SG	1:CYS27:SG

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 71.4 %, Completeness: 99.2 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	99.2 % (127 of 128)	99.2 % (127 of 128)
Backbone	97.5 % (39 of 40)	97.5 % (39 of 40)
Sidechain	100.0 % (88 of 88)	100.0 % (88 of 88)
Aromatic	100.0 % (10 of 10)	100.0 % (10 of 10)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. entity 1

NDXCKXLKXR YXGCEXRCDX PRYEXHCX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 4.0, Details 0.2 mM NA DSS, 1.0 mM NA Designed peptide NC_HEE_D1: Aib turn, Aib helix, N-methyl hairpin mutant, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		0.2 mM
2	Designed peptide NC_HEE_D1: Aib turn, Aib helix, N-methyl hairpin mutant	natural abundance		1.0 mM

Release date

2018-07-29

Citation

Heterogeneous-Backbone Foldamer Mimics of a Computationally Designed, Disulfide-Rich Miniprotein
Cabalteja, C.C., Mihalko, D.S., Horne, W.S.
Chembiochem. (2018), 20, 103-110, PubMed 30326175 , DOI 10.1002/cbic.201800558 , Abstract

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 30497 released on 2018-07-30
    Title Heterogeneous-Backbone Mimics of a Designed Disulfide-Rich Protein: Orn turn
  BMRB: 30498 released on 2018-07-30
    Title Heterogeneous-Backbone Mimics of a Designed Disulfide-Rich Protein: Aib turn, beta3 helix, N-methyl hairpin
  BMRB: 30496 released on 2018-07-29
    Title Heterogeneous-Backbone Mimics of a Designed Disulfide-Rich Protein: Aib turn

Related entities 1. Designed peptide NC HEE D1: Aib turn, Aib helix, N-methyl hairpin mutant, : 1 : 1 : 3 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30499_6e5k.nef
Input source #2: Coordindates	6e5k.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	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:4:CYS:SG	A:18:CYS:SG	unknown	unknown	2.029
A:14:CYS:SG	A:27:CYS:SG	unknown	unknown	2.032

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:ASP:C	1:3:AIB:N	unknown	unknown	n/a
1:3:AIB:C	1:4:CYS:N	unknown	unknown	n/a
1:5:LYS:C	1:6:AIB:N	unknown	unknown	n/a
1:6:AIB:C	1:7:LEU:N	unknown	unknown	n/a
1:8:LYS:C	1:9:AIB:N	unknown	unknown	n/a
1:9:AIB:C	1:10:ARG:N	unknown	unknown	n/a
1:11:TYR:C	1:12:AIB:N	unknown	unknown	n/a
1:12:AIB:C	1:13:GLY:N	unknown	unknown	n/a
1:15:GLU:C	1:16:MVA:N	unknown	unknown	n/a
1:16:MVA:C	1:17:ARG:N	unknown	unknown	n/a
1:19:ASP:C	1:20:DPR:N	unknown	unknown	n/a
1:20:DPR:C	1:21:PRO:N	unknown	unknown	n/a
1:24:GLU:C	1:25:MVA:N	unknown	unknown	n/a
1:25:MVA:C	1:26:HIS:N	unknown	unknown	n/a
1:27:CYS:C	1:28:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	6	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	9	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	12	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	16	MVA	N-METHYLVALINE	Assigned chemical shifts, Distance restraints, Coordinates
A	20	DPR	D-PROLINE	Assigned chemical shifts, Distance restraints, Coordinates
A	25	MVA	N-METHYLVALINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	28	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------
NDXCKXLKXRYXGCEXRCDXPRYEXHCX
||||||||||||||||||||||||||||
NDXCKXLKXRYXGCEXRCDXPRYEXHCX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_30499_6e5k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	17		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	157		100.0 (chain: A, length: 28)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	513 (1)	noe	82.1 (chain: A, length: 28)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	89 (1)	noe	64.3 (chain: A, length: 28)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	26 (1)	hbond	50.0 (chain: A, length: 28)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	Warning	10 (10)	.	50.0 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 157
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID
16	MVA
20	DPR
25	MVA

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	140	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	43	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	97	91.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	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: 28, Sequence coverage: 82.1%
- Total number of restraints: 501
- Weight of restraints: 1.0 (501)
- Potential type of restraints: square-well-parabolic (501)
- Range of distance target values: 1.61, 4.11 (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: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 64.3%
  - Total number of restraints: 80
  - Weight of restraints: 1.0 (80)
  - Potential type of restraints: square-well-parabolic (80)
  - Range of distance target values: 2.21, 4.54 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 50.0%
    - Total number of restraints: 26
    - Weight of restraints: 1.0 (26)
    - Potential type of restraints: square-well-parabolic (26)
    - Range of distance target values: 1.9, 2.9 (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_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 50.0%
- Total number of restraints: 10
- Total number of restraints per polymer type: 10
- Weight of restraints: 1.0 (10)
- Potential type of restraints: square-well-parabolic (10)
- Dihedral angle restraints per residue

Keywords DE NOVO PROTEIN, heterogeneous backbone foldamer

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Found 1 Document (0.47 seconds)

BMRB: 30499

Sample

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. Designed peptide NC HEE D1: Aib turn, Aib helix, N-methyl hairpin mutant, : 1 : 1 : 3 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail