BMRBj - BMREntryMaster

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 5.5, Details 5 mg/mL Design 11_ss, 5 % v/v [U-99% 2H] glycerol, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Design 11_ss	natural abundance		5 mg/mL
2	glycerol	[U-99% 2H]		5 % v/v

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

Release date

2017-12-20

Citation

Comprehensive computational design of ordered peptide macrocycles
Hosseinzadeh, P., Bhardwaj, G., Mulligan, V.K., Shortridge, M.D., Craven, T.W., Pardo-Avila, F., Rettie, S.A., Kim, D.E., Silva, D.A., Ibrahim, Y.M., Webb, I.K., Cort, J.R., Adkins, J.N., Varani, G., Baker, D.
Science (2017), 358, 1461-1466, PubMed 29242347 , DOI 10.1126/science.aap7577 , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30361_6bes.nef
Input source #2: Coordindates	6bes.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	True (see coordinates for details)
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:4:DCY:SG	A:9:DCY:SG	unknown	unknown	2.032

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)
1:1:DAL:C	1:2:GLN:N	unknown	unknown	n/a
1:2:GLN:C	1:3:DPR:N	unknown	unknown	n/a
1:3:DPR:C	1:4:DCY:N	unknown	unknown	n/a
1:4:DCY:C	1:5:DLY:N	unknown	unknown	n/a
1:5:DLY:C	1:6:ASP:N	unknown	unknown	n/a
1:7:SER:C	1:8:DTY:N	unknown	unknown	n/a
1:8:DTY:C	1:9:DCY:N	unknown	unknown	n/a
1:9:DCY:C	1:10:PRO:N	unknown	unknown	n/a
1:10:PRO:C	1:11:DSN:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	DAL	D-ALANINE	Assigned chemical shifts, Coordinates
A	3	DPR	D-PROLINE	Assigned chemical shifts, Distance restraints, Coordinates
A	4	DCY	D-CYSTEINE	Assigned chemical shifts, Coordinates
A	5	DLY	D-LYSINE	Assigned chemical shifts, Coordinates
A	8	DTY	D-TYROSINE	Assigned chemical shifts, Coordinates
A	9	DCY	D-CYSTEINE	Assigned chemical shifts, Coordinates
A	11	DSN	D-SERINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10-
XQXXXDSXXPX
|||||||||||
XQXXXDSXXPX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	11	0	0	100.0

Content subtype: combined_30361_6bes.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	11		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	57		100.0 (chain: A, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	16 (1)	noe	45.5 (chain: A, length: 11)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 57
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID
3	DPR
4	DCY
5	DLY
8	DTY
9	DCY
11	DSN

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	24	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	16	94.1

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 45.5%
- Total number of restraints: 16
- Weight of restraints: 1.0 (16)
- Potential type of restraints: square-well-parabolic (16)
- Range of distance target values: 2.5, 4.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords DE NOVO PROTEIN, de novo, macrocycle

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BMRB: 30361

Sample

Experiments performed 4 experiments Detail

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NMR combined restraints 3 contents Detail