BMRBj - BMREntryMaster

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BMRB: 30647

6PX7

Dg12a

Authors

Agwa, A.J., Schroeder, C.

Assembly

Venom polypeptide

Entity

1. Venom polypeptide (polymer, Thiol state: all disulfide bound), 34 monomers, 3915.500 Da Detail

SQEQRQCKKI GEHCYVADEC CSKRCLFYAA KCVS

Formula weight

3915.5 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS21:SG
2	disulfide	sing	1:CYS14:SG	1:CYS25:SG
3	disulfide	sing	1:CYS20:SG	1:CYS32:SG

Source organism

Dolopus genitalis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.9 %, Completeness (bb): 80.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.9 % (325 of 392)	93.2 % (193 of 207)	66.9 % (99 of 148)	89.2 % (33 of 37)
Backbone	80.4 % (164 of 204)	92.8 % (64 of 69)	66.3 % (67 of 101)	97.1 % (33 of 34)
Sidechain	87.8 % (194 of 221)	93.5 % (129 of 138)	81.3 % (65 of 80)	0.0 % (0 of 3)
Aromatic	46.7 % (14 of 30)	93.3 % (14 of 15)	0.0 % (0 of 15)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. entity 1

SQEQRQCKKI GEHCYVADEC CSKRCLFYAA KCVS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 4, Details 1 mg/mL Dg12a, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Dg12a	natural abundance		1 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6PX7, Strand ID: A Detail

Release date

2019-07-28

Citation

Weaponisation 'on the fly': Convergent recruitment of knottin and defensin peptide scaffolds into the venom of predatory assassin flies
Jin, J., Agwa, A.J., Szanto, T.G., Csoti, A., Panyi, G., Schroeder, C.I., Walker, A.A., King, G.F.
Insect Biochem. Mol. Biol. (2019), 118, 103310-103310, PubMed 31870846 , DOI 10.1016/j.ibmb.2019.103310 , Abstract

Related entities 1. Venom polypeptide, : 1 : 10 entities Detail

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30647_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	1:21:CYS:SG	oxidized, CA 59.256, CB 41.806 ppm	oxidized, CA 57.261, CB 38.041 ppm	n/a
1:14:CYS:SG	1:25:CYS:SG	oxidized, CA 53.01, CB 38.048 ppm	oxidized, CA 59.219, CB 42.261 ppm	n/a
1:20:CYS:SG	1:32:CYS:SG	oxidized, CA 54.593, CB 38.579 ppm	oxidized, CA 54.835, CB 37.968 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30647_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	365		100.0 (chain: 1, length: 34)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 233
  - ¹³C chemical shifts: 99
  - ¹⁵N chemical shifts: 33
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	LYS	HZ1	7.63
8	LYS	HZ2	7.63
8	LYS	HZ3	7.63
9	LYS	HZ1	7.573
9	LYS	HZ2	7.573
9	LYS	HZ3	7.573
23	LYS	HZ1	7.528
23	LYS	HZ2	7.528
23	LYS	HZ3	7.528
31	LYS	HZ1	7.581
31	LYS	HZ2	7.581
31	LYS	HZ3	7.581

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	207	199	96.1
¹³C chemical shifts	148	99	66.9
¹⁵N chemical shifts	39	33	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	68	98.6
¹³C chemical shifts	68	34	50.0
¹⁵N chemical shifts	34	33	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	131	94.9
¹³C chemical shifts	80	65	81.2
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	14	93.3
¹³C chemical shifts	15	0	0.0

Keywords assassin-fly, disulfide-rich, knottin, ultra-stable peptide

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Found 1 Document (0.582 seconds)

BMRB: 30647

Sample

Related entities 1. Venom polypeptide, : 1 : 10 entities Detail

Experiments performed 5 experiments Detail

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Chemical shift validation 3 contents Detail