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BMRB: 25847

2N8E

three-dimensional structure of cyclic PVIIA

Authors

Kwon, S., Schroeder, C., Craik, D.

Assembly

cyclic PVIIA

Entity

1. cyclic PVIIA (polymer, Thiol state: all disulfide bound), 34 monomers, 3887.455 Da Detail

CRIXNQKCFQ HLDDCCSRKC NRFNKCVLPE TGGG

Formula weight

3887.455 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS1:SG	1:CYS16:SG
2	disulfide	sing	1:CYS8:SG	1:CYS20:SG
3	disulfide	sing	1:CYS15:SG	1:CYS26:SG

Source organism

Conus purpurascens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 84.2 %, Completeness (bb): 82.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.2 % (320 of 380)	94.6 % (192 of 203)	65.7 % (92 of 140)	97.3 % (36 of 37)
Backbone	82.7 % (162 of 196)	100.0 % (68 of 68)	65.6 % (63 of 96)	96.9 % (31 of 32)
Sidechain	87.9 % (188 of 214)	91.9 % (124 of 135)	79.7 % (59 of 74)	100.0 % (5 of 5)
Aromatic	29.2 % (7 of 24)	58.3 % (7 of 12)	0.0 % (0 of 12)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. entity

CRIXNQKCFQ HLDDCCSRKC NRFNKCVLPE TGGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2N8E, Strand ID: A Detail

Release date

2016-08-21

Citation

Efficient enzymatic cyclization of an inhibitory cystine knot-containing peptide
Kwon, S., Bosmans, F., Kaas, Q., Cheneval, O., Conibear, A.C., Schroeder, C.I., Craik, D.J.
Biotechnol. Bioeng. (2016), 113, 2202-2212, PubMed 27093300 , DOI 10.1002/bit.25993 , Abstract

Related entities 1. cyclic PVIIA, : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25847_2n8e.nef
Input source #2: Coordindates	2n8e.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	True (see coodinates for details)
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)
A:1:CYS:SG	A:16:CYS:SG	oxidized, CA 54.193, CB 42.299 ppm	oxidized, CA 57.373, CB 38.944 ppm	2.027
A:8:CYS:SG	A:20:CYS:SG	oxidized, CA 53.359, CB 46.978 ppm	oxidized, CA 54.075, CB 41.686 ppm	2.03
A:15:CYS:SG	A:26:CYS:SG	oxidized, CA 55.991, CB 36.802 ppm	oxidized, CA 53.786, CB 37.642 ppm	2.034

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:3:ILE:C	1:4:HYP:N	unknown	unknown	n/a
1:4:HYP:C	1:5:ASN:N	unknown	unknown	n/a
1:34:GLY:C	1:1:CYS:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	4	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30----
CRIXNQKCFQHLDDCCSRKCNRFNKCVLPETGGG
||||||||||||||||||||||||||||||||||
CRIXNQKCFQHLDDCCSRKCNRFNKCVLPETGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_25847_2n8e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	344		100.0 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	526 (1)	noe	97.1 (chain: A, length: 34)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	8 (1)	hbond	17.6 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	37 (37)	.	70.6 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 210
  - ¹³C chemical shifts: 93
  - ¹⁵N chemical shifts: 41
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	LYS	HZ1	7.574
7	LYS	HZ2	7.574
7	LYS	HZ3	7.574
7	LYS	NZ	113.011
11	HIS	HD1	7.286
19	LYS	HZ1	7.858
19	LYS	HZ2	7.858
19	LYS	HZ3	7.858
19	LYS	NZ	121.189
25	LYS	HZ1	7.498
25	LYS	HZ2	7.498
25	LYS	HZ3	7.498

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	209	197	94.3
¹³C chemical shifts	145	93	64.1
¹⁵N chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	68	98.6
¹³C chemical shifts	68	31	45.6
¹⁵N chemical shifts	32	31	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	129	92.1
¹³C chemical shifts	77	62	80.5
¹⁵N chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0
¹³C chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	7	58.3
¹³C chemical shifts	12	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of restraints: 518
- Weight of restraints: 1.0 (518)
- Potential type of restraints: square-well-parabolic (518)
- Range of distance target values: 1.17, 2.75 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 17.6%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 1.0, 1.5 (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: 34, Sequence coverage: 70.6%
- Total number of restraints: 37
- Total number of restraints per polymer type: 37
- Weight of restraints: 1.0 (37)
- Potential type of restraints: square-well-parabolic (37)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords inhibitor cystine knot

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Found 1 Document (0.553 seconds)

BMRB: 25847

Sample

Related entities 1. cyclic PVIIA, : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

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NMR combined restraints 5 contents Detail