BMRBj - BMREntryMaster

Found 1 Document (0.589 seconds)

BMRB: 30749

6WQL

Solution structure of the seed peptide C2 (VBP-1) from pumpkin

Authors

Payne, C.P., Rosengren, K.J.

Assembly

Seed peptide C2 (VBP-1)

Entity

1. Seed peptide C2 (VBP-1) (polymer, Thiol state: all disulfide bound), 49 monomers, 5833.368 Da Detail

XRGSPRAEYE VCRLRCQVAE RGVEQQRKCE QVCEERLRER EQGRGEDVD

Formula weight

5833.368 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

Cucurbita maxima

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 73.7 %, Completeness (bb): 72.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.7 % (414 of 562)	94.7 % (284 of 300)	44.0 % (88 of 200)	67.7 % (42 of 62)
Backbone	72.7 % (208 of 286)	100.0 % (99 of 99)	47.9 % (67 of 140)	89.4 % (42 of 47)
Sidechain	70.3 % (225 of 320)	92.0 % (185 of 201)	38.5 % (40 of 104)	0.0 % (0 of 15)
Aromatic	50.0 % (4 of 8)	100.0 % (4 of 4)	0.0 % (0 of 4)
Methyl	78.1 % (25 of 32)	68.8 % (11 of 16)	87.5 % (14 of 16)

1. entity 1

XRGSPRAEYE VCRLRCQVAE RGVEQQRKCE QVCEERLRER EQGRGEDVD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5, Details 2 mg/mL C2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	C2	natural abundance		2 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6WQL, 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

Related entities 1. Seed peptide C2 (VBP-1), : 1 : 8 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30749_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)
1:12:CYS:SG	1:33:CYS:SG	oxidized, CA 59.957, CB 36.712 ppm	oxidized, CA 57.045, CB 36.237 ppm	n/a
1:16:CYS:SG	1:29:CYS:SG	oxidized, CA 56.59, CB 37.166 ppm	oxidized, CA 59.74, CB 35.245 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: bmr30749_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	441		100.0 (chain: 1, length: 49)
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: 49, Sequence coverage: 100.0%
- Total number of assignments
  - ¹⁵N chemical shifts: 43
  - ¹³C chemical shifts: 87
  - ¹H chemical shifts: 311
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	63	43	68.3
¹³C chemical shifts	203	87	42.9
¹H chemical shifts	306	289	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	48	43	89.6
¹³C chemical shifts	97	47	48.5
¹H chemical shifts	101	100	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	15	0	0.0
¹³C chemical shifts	106	40	37.7
¹H chemical shifts	205	189	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	16	14	87.5
¹H chemical shifts	16	11	68.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	4	0	0.0
¹H chemical shifts	4	4	100.0

Keywords PLANT PROTEIN, vicilin-buried peptide

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.589 seconds)

BMRB: 30749

Sample

Related entities 1. Seed peptide C2 (VBP-1), : 1 : 8 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail