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BMRB: 30580

6O3S

NMR solution structure of vicilin-buried peptide-8 (VBP-8)

Authors

Rosengren, K.J., Payne, C.

Assembly

Ribosome-inactivating protein luffin P1 (E.C.3.2.2.22)

Entity

1. Ribosome-inactivating protein luffin P1 (E.C.3.2.2.22) (polymer, Thiol state: all disulfide bound), 47 monomers, 5698.345 Da Detail

PRGSPRTEYE ACRVRCQVAE HGVERQRRCQ QVCEKRLRER EGRREVD

Formula weight

5698.345 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS12:SG	1:CYS33:SG
2	disulfide	sing	1:CYS16:SG	1:CYS29:SG

Source organism

Luffa aegyptiaca

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 76.8 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.8 % (423 of 551)	91.0 % (274 of 301)	52.2 % (105 of 201)	89.8 % (44 of 49)
Backbone	80.9 % (225 of 278)	97.9 % (93 of 95)	63.8 % (88 of 138)	97.8 % (44 of 45)
Sidechain	76.0 % (241 of 317)	87.9 % (181 of 206)	56.1 % (60 of 107)	0.0 % (0 of 4)
Aromatic	33.3 % (4 of 12)	66.7 % (4 of 6)	0.0 % (0 of 6)
Methyl	80.0 % (24 of 30)	66.7 % (10 of 15)	93.3 % (14 of 15)

1. entity 1

PRGSPRTEYE ACRVRCQVAE HGVERQRRCQ QVCEKRLRER EGRREVD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6O3S, Strand ID: A Detail

Release date

2019-04-14

Citation

An Ancient Peptide Family Buried within Vicilin Precursors
Zhang, J., Payne, C.D., Pouvreau, B., Schaefer, H., Fisher, M.F., Taylor, N.L., Berkowitz, O., Whelan, J., Rosengren, K.J., Mylne, J.S.
ACS Chem. Biol. (2019), 14, 979-993, PubMed 30973714 , DOI 10.1021/acschembio.9b00167 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30579 released on 2019-04-14
Title NMR solution structure of vicilin-buried peptide-8 (VBP-8)

Related entities 1. Ribosome-inactivating protein luffin P1 (E.C.3.2.2.22), : 1 : 1 : 8 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

2 2D 1H-1H NOESY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

3 2D 1H-15N HSQC

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

4 2D 1H-13C HSQC

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

5 2D 1H-1H NOESY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

6 2D 1H-1H NOESY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

7 2D 1H-1H NOESY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

8 2D 1H-1H NOESY

Instrument

Bruker Avence III - 700 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 4 (±0.2), Details 2 mg/mL Luffin P1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Luffin P1	natural abundance		2 mg/mL

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30580_6o3s.nef
Input source #2: Coordindates	6o3s.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	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:12:CYS:SG	A:33:CYS:SG	oxidized, CA 58.124, CB 36.84 ppm	oxidized, CA 57.049, CB 36.364 ppm	2.022
A:16:CYS:SG	A:29:CYS:SG	oxidized, CA 53.98, CB 37.316 ppm	oxidized, CA 56.772, CB 35.041 ppm	2.024

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--------20--------30--------40-------
PRGSPRTEYEACRVRCQVAEHGVERQRRCQQVCEKRLREREGRREVD
|||||||||||||||||||||||||||||||||||||||||||||||
PRGSPRTEYEACRVRCQVAEHGVERQRRCQQVCEKRLREREGRREVD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_30580_6o3s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	428		100.0 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Error	588 (1)	noe	100.0 (chain: A, length: 47)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	42 (1)	hbond	63.8 (chain: A, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	72 (72)	.	83.0 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 281
  - ¹³C chemical shifts: 103
  - ¹⁵N chemical shifts: 44
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of restraints: 588
- Weight of restraints: 1.0 (588)
- Potential type of restraints: square-well-parabolic (588)
- Range of distance target values: 2.23, 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: 47, Sequence coverage: 63.8%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 1.15, 1.65 (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: 47, Sequence coverage: 83.0%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HYDROLASE, PLANT PROTEIN, seed peptide