BMRBj - BMREntryMaster

Found 1 Document (1.023 seconds)

BMRB: 30000

5GAJ

Solution NMR structure of De novo designed PLOOP2X3_50 fold protein, Northeast Structural Genomics Consortium (NESG) target OR258

Authors

Liu, G., Castelllanos, J., Koga, R., Koga, N., Xiao, R., Pederson, K., Janjua, H., Kohan, E., Acton, T.B., Kornhaber, G., Everett, J., Baker, D., Montelione, G.T.

Assembly

DE NOVO DESIGNED PROTEIN OR258

Entity

1. DE NOVO DESIGNED PROTEIN OR258 (polymer), 134 monomers, 15737.81 Da Detail

MGTVVIVVSR DERILEELLE VVLKSDPNVK TVRTDDKEKV KEEIEKARKQ GRPIVIFIRG ATEEVVRDIV EYAQKEGLRV LVIMVDQDQE ELERIYEQLK KDGVDVRVTD NEDEAKKRLK ELLEKVLEHH HHHH

Formula weight

15737.81 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 95.6 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.6 % (1547 of 1619)	95.9 % (817 of 852)	95.4 % (599 of 628)	94.2 % (131 of 139)
Backbone	95.5 % (764 of 800)	96.3 % (261 of 271)	95.5 % (379 of 397)	93.9 % (124 of 132)
Sidechain	95.7 % (907 of 948)	95.7 % (556 of 581)	95.6 % (344 of 360)	100.0 % (7 of 7)
Aromatic	72.0 % (36 of 50)	80.0 % (20 of 25)	64.0 % (16 of 25)
Methyl	100.0 % (182 of 182)	100.0 % (91 of 91)	100.0 % (91 of 91)

1. entity 1

MGTVVIVVSR DERILEELLE VVLKSDPNVK TVRTDDKEKV KEEIEKARKQ GRPIVIFIRG ATEEVVRDIV EYAQKEGLRV LVIMVDQDQE ELERIYEQLK KDGVDVRVTD NEDEAKKRLK ELLEKVLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.89 mM [U-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.89 mM [5%-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DTT	natural abundance	5 mM
7	OR258	[5%-13C; U-15N]	0.89 mM
8	TRIS-HCl	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.45 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5GAJ, Strand ID: A Detail

Release date

2016-06-16

Citation

Role of backbone strain in de novo design of complex α/β protein structures
Koga, N., Koga, R., Liu, G., Castellanos, J., Montelione, G.T., Baker, D.
Nat. Commun. (2021), 12, 3921-3921, PubMed 34168113 , DOI 10.1038/s41467-021-24050-7 , Abstract

Related entities 1. DE NOVO DESIGNED PROTEIN OR258, : 1 : 2 : 10 entities Detail

Experiments performed 7 experiments Detail

1 3D simutalneous 13C-aromatic, 13C-aliphatic, 15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.89 mM [U-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

2 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

4 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	5 mM
2	OR258	[U-13C; U-15N]	0.89 mM
3	TRIS-HCl	natural abundance	10 mM
4	sodium azide	natural abundance	0.02 %
5	sodium chloride	natural abundance	100 mM

7 2D 1H-13C HSQC methyl

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.89 mM [5%-13C; U-15N] OR258, 5 mM DTT, 100 mM sodium chloride, 10 mM TRIS-HCl, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DTT	natural abundance	5 mM
7	OR258	[5%-13C; U-15N]	0.89 mM
8	TRIS-HCl	natural abundance	10 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	100 mM

nullKeywords DE NOVO PROTEIN, NESG, Northeast Structural Genomics Consortium, PSI-Biology

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Found 1 Document (1.023 seconds)

BMRB: 30000

Sample #1

Sample #2

Chemical shift reference

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Chemical shift reference

Chemical shift reference

Related entities 1. DE NOVO DESIGNED PROTEIN OR258, : 1 : 2 : 10 entities Detail

Experiments performed 7 experiments Detail

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