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BMRB: 30141

5KWP

NMR Solution Structure of Designed Peptide NC_EEH_D2

Authors

Harvey, P.J., Craik, D.J.

Assembly

Designed peptide NC EEH D2

Entity

1. Designed peptide NC EEH D2 (polymer, Thiol state: all disulfide bound), 27 monomers, 2974.352 Da Detail

TCVECXXVKV CRPDPEEARR EAEERCX

Formula weight

2974.352 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.9 %, Completeness: 90.1 %, Completeness (bb): 81.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (237 of 263)	99.3 % (140 of 141)	76.0 % (76 of 100)	95.5 % (21 of 22)
Backbone	81.4 % (114 of 140)	97.8 % (45 of 46)	66.7 % (48 of 72)	95.5 % (21 of 22)
Sidechain	99.3 % (146 of 147)	100.0 % (95 of 95)	98.1 % (51 of 52)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. entity 1

TCVECXXVKV CRPDPEEARR EAEERCX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 null, Temperature 298 (±0.1) K, pH 3.0 (±0.1), Details 1.0 mg/mL design peptide NC_EEH_D2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	design peptide NC_EEH_D2	natural abundance		1.0 mg/mL

Sample #2

Solvent system 100% D2O, Pressure 1 null, Temperature 298 (±0.1) K, pH 3.0 (±0.1), Details 1.0 mg/mL design peptide NC_EEH_D2, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	design peptide NC_EEH_D2	natural abundance		1.0 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 5KWP, Strand ID: A Detail

Release date

2016-09-15

Citation

Accurate de novo design of hyperstable constrained peptides
Bhardwaj, G., Mulligan, V.K., Bahl, C.D., Gilmore, J.M., Harvey, P.J., Cheneval, O., Buchko, G.W., Pulavarti, S.V., Kaas, Q., Eletsky, A., Huang, P.S., Johnsen, W.A., Greisen, P.J., Rocklin, G.J., Song, Y., Linsky, T.W., Watkins, A., Rettie, S.A., Xu, X., Carter, L.P., Bonneau, R., Olson, J.M., Coutsias, E., Correnti, C.E., Szyperski, T., Craik, D.J., Baker, D.
Nature (2016), 538, 329-335, PubMed 27626386 , DOI 10.1038/nature19791 , Abstract

Entries sharing articles BMRB: 12 entries Detail

  BMRB: 30204 released on 2017-03-16
    Title Solution structure of the de novo mini protein gHH_44
  BMRB: 30067 released on 2016-09-21
    Title Solution structure of the de novo miniprotein EHE_06
  BMRB: 30069 released on 2016-09-21
    Title Solution structure of the de novo miniprotein EEHE_02
  BMRB: 30138 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_HEE_D1
  BMRB: 30140 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_EHE_D1
  BMRB: 30142 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_EEH_D1
  BMRB: 30143 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHH_D1
  BMRB: 30144 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHh_DL_D1
  BMRB: 30145 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHHH_D1
  BMRB: 30146 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cEE_D1
  BMRB: 26045 released on 2016-09-12
    Title Solution structure of the de novo mini protein HHH_06
  BMRB: 26046 released on 2016-09-12
    Title Solution structure of the de novo mini protein EEH_04

Related entities 1. Designed peptide NC EEH D2, : 6 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_30141_5kwp.nef
Input source #2: Coordindates	5kwp.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:2:CYS:SG	A:11:CYS:SG	oxidized, CA 55.57, CB 46.545 ppm	oxidized, CA 54.756, CB 46.43 ppm	2.028
A:5:CYS:SG	A:26:CYS:SG	oxidized, CB 41.688 ppm	oxidized, CA 57.508, CB 44.412 ppm	2.034

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)
1:5:CYS:C	1:6:DAL:N	unknown	unknown	n/a
1:6:DAL:C	1:7:DPR:N	unknown	unknown	n/a
1:7:DPR:C	1:8:VAL:N	unknown	unknown	n/a
1:26:CYS:C	1:27:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	DAL	D-ALANINE	Assigned chemical shifts, Torsion angle restraints, Coordinates
A	7	DPR	D-PROLINE	Assigned chemical shifts, Torsion angle restraints, Coordinates
A	27	NH2	AMINO GROUP	Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20-------
TCVECXXVKVCRPDPEEARREAEERCX
|||||||||||||||||||||||||||
TCVECXXVKVCRPDPEEARREAEERCX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_30141_5kwp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	255		96.3 (chain: A, length: 27)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	319 (1)	noe	88.9 (chain: A, length: 27)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	20 (1)	hbond	51.9 (chain: A, length: 27)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	45 (45)	.	100.0 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 153
  - ¹³C chemical shifts: 80
  - ¹⁵N chemical shifts: 22
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Comp_index_ID	Comp_ID
7	DPR

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	LYS	HZ1	7.552
9	LYS	HZ2	7.552
9	LYS	HZ3	7.552

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	146	143	97.9
¹³C chemical shifts	102	76	74.5
¹⁵N chemical shifts	28	22	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	47	97.9
¹³C chemical shifts	49	24	49.0
¹⁵N chemical shifts	24	22	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	96	98.0
¹³C chemical shifts	53	52	98.1
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	10	100.0

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: 27, Sequence coverage: 88.9%
- Total number of restraints: 317
- Weight of restraints: 1.0 (317)
- Potential type of restraints: square-well-parabolic (317)
- Range of distance target values: 2.01, 3.65 (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: 27, Sequence coverage: 51.9%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: square-well-parabolic (20)
  - Range of distance target values: 1.0, 1.5 (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: 27, Sequence coverage: 100.0%
- Total number of restraints: 45
- Total number of restraints per polymer type: 45
- Weight of restraints: 1.0 (45)
- Potential type of restraints: square-well-parabolic (45)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords de novo protein, synthetic designed peptide

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Found 1 Document (0.595 seconds)

BMRB: 30141

Sample #1

Sample #2

Entries sharing articles BMRB: 12 entries Detail

Related entities 1. Designed peptide NC EEH D2, : 6 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Sample

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Sample

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NMR combined restraints 5 contents Detail