BMRBj - BMREntryMaster

Found 1 Document (0.575 seconds)

BMRB: 30748

6WQJ

Solution structure of vicilin-buried peptide-10 from cucumber

Authors

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

Assembly

Vicilin-buried peptide-10

Entity

1. Vicilin-buried peptide-10 (polymer, Thiol state: all disulfide bound), 35 monomers, 4321.787 Da Detail

XKETEICRQW CQVMKPQGGE EQRRCQQECE ERLRD

Formula weight

4321.787 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS29:SG
2	disulfide	sing	1:CYS11:SG	1:CYS25:SG

Source organism

Cucumis sativus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 77.3 %, Completeness (bb): 78.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	77.3 % (290 of 375)	90.8 % (207 of 228)	56.5 % (83 of 147)
Backbone	78.1 % (132 of 169)	100.0 % (69 of 69)	63.0 % (63 of 100)
Sidechain	78.2 % (186 of 238)	86.8 % (138 of 159)	60.8 % (48 of 79)
Aromatic	18.2 % (2 of 11)	33.3 % (2 of 6)	0.0 % (0 of 5)
Methyl	42.9 % (6 of 14)	85.7 % (6 of 7)	0.0 % (0 of 7)

1. entity 1

XKETEICRQW CQVMKPQGGE EQRRCQQECE ERLRD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5 (±0.2), Details 1.5 mg/mL VBP-10, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	VBP-10	natural abundance		1.5 mg/mL

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5 (±0.2), Details 1.5 mg/mL VBP-10, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	VBP-10	natural abundance		1.5 mg/mL

Protein Blocks Logo

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

Release date

2020-05-25

Citation

Defining the Familial Fold of the Vicilin-Buried Peptide Family
Payne, C.D., Vadlamani, G., Fisher, M.F., Zhang, J., Clark, R.J., Mylne, J.S., Rosengren, K.J.
J. Nat. Prod. (2020), 83, 3030-3040, PubMed 32997497 , DOI 10.1021/acs.jnatprod.0c00594 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30749 released on 2020-05-25
Title Solution structure of the seed peptide C2 (VBP-1) from pumpkin

Related entities 1. Vicilin-buried peptide-10, : 1 : 2 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30748_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	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:CYS:SG	1:29:CYS:SG	oxidized, CA 52.862, CB 41.698 ppm	oxidized, CA 58.509, CB 43.119 ppm	n/a
1:11:CYS:SG	1:25:CYS:SG	oxidized, CA 55.515, CB 41.736 ppm	oxidized, CA 56.375, CB 43.157 ppm	n/a

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	1	PCA	PYROGLUTAMIC ACID	Assigned chemical shifts

Content subtype: bmr30748_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	306		100.0 (chain: 1, length: 35)
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: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 225
  - ¹³C chemical shifts: 81
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	234	213	91.0
¹³C chemical shifts	150	81	54.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	71	100.0
¹³C chemical shifts	69	33	47.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	163	142	87.1
¹³C chemical shifts	81	48	59.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	6	75.0
¹³C chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	2	33.3
¹³C chemical shifts	5	0	0.0

Keywords PLANT PROTEIN

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Found 1 Document (0.575 seconds)

BMRB: 30748

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Vicilin-buried peptide-10, : 1 : 2 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail