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BMRB: 30828

7L54

Solution NMR structure of the monomeric form of the cyclic plant protein PDP-23 in CD3CN/H2O

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: 72.7 %, Completeness (bb): 71.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.7 % (229 of 315)	99.4 % (160 of 161)	38.6 % (49 of 127)	74.1 % (20 of 27)
Backbone	71.2 % (114 of 160)	100.0 % (55 of 55)	48.1 % (39 of 81)	83.3 % (20 of 24)
Sidechain	76.7 % (138 of 180)	99.1 % (105 of 106)	46.5 % (33 of 71)	0.0 % (0 of 3)
Aromatic	48.5 % (32 of 66)	97.0 % (32 of 33)	0.0 % (0 of 31)	0.0 % (0 of 2)
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 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

Protein Blocks Logo

Calculated from 20 models in PDB: 7L53, Strand ID: A Detail

Release date

2021-01-20

Citation

A chameleonic macrocyclic peptide with drug delivery applications
Payne, C.D., Franke, B.F., 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

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

Experiments performed 9 experiments Detail

1 1D

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

2 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

3 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

4 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

5 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 298 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

6 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 288 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

7 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 308 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

8 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 303 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

9 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 80% H2O/20% ACN, Pressure 1 atm, Temperature 293 K, pH 4, Details 1.0 mg/L PDP-23, 80% H2O/20% ACN

#	Name	Isotope labeling	Type	Concentration
1	PDP-23	natural abundance		1.0 mg/L

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30828_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	oxidized, CA 55.436, CB 48.032 ppm	oxidized, CA 55.517, CB 48.008 ppm	n/a
1:14:CYS:SG	1:25:CYS:SG	oxidized, CA 55.706, CB 48.603 ppm	oxidized, CA 55.032, CB 46.966 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30828_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	241		100.0 (chain: 1, length: 28)
1	Chemical shift references	chem_shift_reference_1	OK	3		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: 172
  - ¹³C chemical shifts: 49
  - ¹⁵N chemical shifts: 20
- 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, hydrophobic core, macrocyclic peptide