BMRBj - BMREntryMaster

Found 1 Document (0.675 seconds)

BMRB: 26045

2ND2

Solution structure of the de novo mini protein HHH_06

Authors

Eletsky, A., Bahl, C.D., Gilmore, J.M., Buchko, G.W., Baker, D.

Assembly

HHH 06

Entity

1. HHH 06 (polymer, Thiol state: all disulfide bound), 44 monomers, 5119.811 Da Detail

APCEDLKERL KKLGMSEECR QRLEKMCKEG TSEDAERMAR NCES

Formula weight

5119.811 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS27:SG
2	disulfide	sing	1:CYS19:SG	1:CYS42:SG

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.1 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.1 % (470 of 505)	97.1 % (266 of 274)	85.5 % (159 of 186)	100.0 % (45 of 45)
Backbone	95.8 % (251 of 262)	97.8 % (87 of 89)	93.1 % (121 of 130)	100.0 % (43 of 43)
Sidechain	89.1 % (254 of 285)	96.8 % (179 of 185)	74.5 % (73 of 98)	100.0 % (2 of 2)
Methyl	79.2 % (19 of 24)	100.0 % (12 of 12)	58.3 % (7 of 12)

1. HHH 06

APCEDLKERL KKLGMSEECR QRLEKMCKEG TSEDAERMAR NCES

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details [U-100 % 15N] labeled HHH_06

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	4 uM
3	D2O	[U-99% 2H]	10 %
4	sodium azide	natural abundance	0.02 %
5	HHH_06	[U-100% 15N]	1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2ND2, Strand ID: A Detail

Release date

2016-09-12

Citation

Accurate de novo design of hyperstable constrained peptides
Bhardwaj, G., Mulligan, V.K., Bahl, C.D., Gilmore, J.M., Harvey, P.J., Cheneval, O., Buchko, G.W., Pulavarti, S.V., Kaas, Q., Eletsky, A., Huang, P.S., Johnsen, W.A., Greisen, P.J., Rocklin, G.J., Song, Y., Linsky, T.W., Watkins, A., Rettie, S.A., Xu, X., Carter, L.P., Bonneau, R., Olson, J.M., Coutsias, E., Correnti, C.E., Szyperski, T., Craik, D.J., Baker, D.
Nature (2016), 538, 329-335, PubMed 27626386 , DOI 10.1038/nature19791 , Abstract

Entries sharing articles BMRB: 12 entries Detail

  BMRB: 30204 released on 2017-03-16
    Title Solution structure of the de novo mini protein gHH_44
  BMRB: 30067 released on 2016-09-21
    Title Solution structure of the de novo miniprotein EHE_06
  BMRB: 30069 released on 2016-09-21
    Title Solution structure of the de novo miniprotein EEHE_02
  BMRB: 30138 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_HEE_D1
  BMRB: 30140 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_EHE_D1
  BMRB: 30141 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_EEH_D2
  BMRB: 30142 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_EEH_D1
  BMRB: 30143 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHH_D1
  BMRB: 30144 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHh_DL_D1
  BMRB: 30145 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cHHH_D1
  BMRB: 30146 released on 2016-09-15
    Title NMR Solution Structure of Designed Peptide NC_cEE_D1
  BMRB: 26046 released on 2016-09-12
    Title Solution structure of the de novo mini protein EEH_04

Related entities 1. HHH 06, : 4 entities Detail

Experiments performed 11 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_26045_2nd2.nef
Input source #2: Coordindates	2nd2.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	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)
A:3:CYS:SG	A:27:CYS:SG	oxidized, CA 57.465, CB 39.971 ppm	oxidized, CA 59.277, CB 40.302 ppm	2.019
A:19:CYS:SG	A:42:CYS:SG	oxidized, CA 59.285, CB 40.375 ppm	oxidized, CA 57.045, CB 41.719 ppm	2.029

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

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40----
APCEDLKERLKKLGMSEECRQRLEKMCKEGTSEDAERMARNCES
||||||||||||||||||||||||||||||||||||||||||||
APCEDLKERLKKLGMSEECRQRLEKMCKEGTSEDAERMARNCES

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_26045_2nd2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	477		100.0 (chain: A, length: 44)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1125 (1)	noe	100.0 (chain: A, length: 44)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	54 (54)	.	75.0 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 273
  - ¹³C chemical shifts: 155
  - ¹⁵N chemical shifts: 49
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	274	273	99.6
¹³C chemical shifts	186	155	83.3
¹⁵N chemical shifts	50	49	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	88	98.9
¹³C chemical shifts	88	86	97.7
¹⁵N chemical shifts	43	42	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	185	100.0
¹³C chemical shifts	98	69	70.4
¹⁵N chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	10	66.7

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: 44, Sequence coverage: 100.0%
- Total number of restraints: 1123
- Weight of restraints: 1.0 (1123)
- Potential type of restraints: square-well-parabolic (1123)
- Range of distance target values: 1.31, 2.89 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 75.0%
- Total number of restraints: 54
- Total number of restraints per polymer type: 54
- Weight of restraints: 1.0 (54)
- Potential type of restraints: square-well-parabolic (54)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, Solution structure, engineered protein

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 (0.675 seconds)

BMRB: 26045

Sample

Entries sharing articles BMRB: 12 entries Detail

Related entities 1. HHH 06, : 4 entities Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail