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BMRB: 30830

7L54

Solution NMR structure of the cyclic plant protein PDP-23 in DPC micelles

Authors

Payne, C.D., Rosengren, K.J.

Assembly

Cyclic plant protein PDP-23

Entity

1. Cyclic plant protein PDP-23 (polymer, Thiol state: all disulfide bound), 28 monomers, 3132.487 Da Detail

GFCWHHSCVP SGTCADFPWP LGHQCFPD

Formula weight

3132.487 Da

Entity Connection

disulfide 2, covalent 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS8:SG
2	disulfide	sing	1:CYS14:SG	1:CYS25:SG
3	covalent	sing	1:GLY1:N	1:ASP28:C

Source organism

Exptl. method

Refine. method

simulated annealingsimulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 68.1 %, Completeness (bb): 67.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	68.1 % (196 of 288)	98.1 % (158 of 161)	29.9 % (38 of 127)
Backbone	67.6 % (92 of 136)	100.0 % (55 of 55)	45.7 % (37 of 81)
Sidechain	67.2 % (119 of 177)	97.2 % (103 of 106)	22.5 % (16 of 71)
Aromatic	48.4 % (31 of 64)	93.9 % (31 of 33)	0.0 % (0 of 31)
Methyl	58.3 % (7 of 12)	100.0 % (6 of 6)	16.7 % (1 of 6)

1. entity 1

GFCWHHSCVP SGTCADFPWP LGHQCFPD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 7L55, Strand ID: A Detail

Release date

2021-01-20

Citation

A chameleonic macrocyclic peptide with drug delivery applications
Payne, C.D., Franke, B., Fisher, M.F., Hajiaghaalipour, F., McAleese, C.E., Song, A., Eliasson, C., Zhang, J., Jayasena, A.S., Vadlamani, G., Clark, R.J., Minchin, R.F., Mylne, J.S., Rosengren, K.J.
Chem. Sci. (2021), 12, 6670-6683, PubMed 34040741 , DOI 10.1039/d1sc00692d , Abstract

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 30827 released on 2021-01-20
    Title Solution NMR structure of the dimeric form of the cyclic plant protein PDP-23 in H2O
  BMRB: 30828 released on 2021-01-20
    Title Solution NMR structure of the monomeric form of the cyclic plant protein PDP-23 in CD3CN/H2O
  BMRB: 30829 released on 2021-01-20
    Title Solution NMR structure of the cyclic plant protein PDP-23 in SDS micelles

Related entities 1. Cyclic plant protein PDP-23, : 1 : 4 : 6 entities Detail

Experiments performed 8 experiments Detail

1 1D

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

2 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

3 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

4 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

5 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

6 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

7 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

8 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5, Details 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		2 mg/mL
2	DPC	natural abundance		12 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30830_3.str
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)
1:3:CYS:SG	1:8:CYS:SG	unknown, CA 55.005 ppm	oxidized 89.3%, reduced 10.7%, CA 55.14, CB 33.87 ppm	n/a
1:14:CYS:SG	1:25:CYS:SG	unknown, CA 55.262 ppm	oxidized, CB 47.491 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30830_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	207		100.0 (chain: 1, length: 28)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 28, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 170
  - ¹³C chemical shifts: 37
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords PLANT PROTEIN, macrocycle, paws derived peptide