BMRBj - BMREntryMaster

Found 1 Document (1.703 seconds)

BMRB: 7101

2GJH

Mistranslation of a computationally designed protein yields an exceptionally stable homodimer: Implications for protein evolution and engineering.

Authors

Dantas, G.

Assembly

Designed protein TOP7

Entity

1. Designed protein TOP7 (polymer, Thiol state: not present), 62 monomers, 7036.807 × 2 Da Detail

MERVRISITA RTKKEAEKFA AILIKVFAEL GYNDINVTWD GDTVTVEGQL EGGSLEHHHH HH

Total weight

14073.614 Da

Max. entity weight

7036.807 Da

Exptl. method

NMR

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 81.9 %, Completeness (bb): 87.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.9 % (585 of 714)	83.9 % (307 of 366)	78.0 % (220 of 282)	87.9 % (58 of 66)
Backbone	87.4 % (325 of 372)	88.4 % (114 of 129)	86.7 % (157 of 181)	87.1 % (54 of 62)
Sidechain	77.7 % (310 of 399)	81.4 % (193 of 237)	71.5 % (113 of 158)	100.0 % (4 of 4)
Aromatic	23.4 % (15 of 64)	43.8 % (14 of 32)	0.0 % (0 of 31)	100.0 % (1 of 1)
Methyl	97.4 % (74 of 76)	94.7 % (36 of 38)	100.0 % (38 of 38)

1. Designed protein TOP7

MERVRISITA RTKKEAEKFA AILIKVFAEL GYNDINVTWD GDTVTVEGQL EGGSLEHHHH HH

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
1	Designed protein TOP7	1 mM
2	phosphate buffer	25 mM
3	H2O	90 %
4	D2O	10 %

LACS Plot; CA

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

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2006-11-16

Citation

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution
Dantas, G., Watters, A.L., Lunde, B.M., Eletr, Z.M., Isern, N.G., Roseman, T., Lipfert, J., Doniach, S., Tompa, M., Kuhlman, B., Stoddard, B.L., Varani, G., Baker, D.
J. Mol. Biol. (2006), 362, 1004-1024, PubMed 16949611 , DOI 10.1016/j.jmb.2006.07.092 , Abstract

Related entities 1. Designed protein TOP7, : 1 : 10 entities Detail

Experiments performed 4 experiments Detail

1 2D NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
1	Designed protein TOP7	1 mM
2	phosphate buffer	25 mM
3	H2O	90 %
4	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
5	Designed protein TOP7	1 mM
6	phosphate buffer	25 mM
7	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Designed protein TOP7	[U-15N; U-13C]	1 mM
9	phosphate buffer		25 mM
10	H2O		90 %
11	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
12	Designed protein TOP7	[U-15N]	1 mM
13	phosphate buffer		25 mM
14	H2O		90 %
15	D2O		10 %

2 3D 13C-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
1	Designed protein TOP7	1 mM
2	phosphate buffer	25 mM
3	H2O	90 %
4	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
5	Designed protein TOP7	1 mM
6	phosphate buffer	25 mM
7	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Designed protein TOP7	[U-15N; U-13C]	1 mM
9	phosphate buffer		25 mM
10	H2O		90 %
11	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
12	Designed protein TOP7	[U-15N]	1 mM
13	phosphate buffer		25 mM
14	H2O		90 %
15	D2O		10 %

3 3D 15N-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
1	Designed protein TOP7	1 mM
2	phosphate buffer	25 mM
3	H2O	90 %
4	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
5	Designed protein TOP7	1 mM
6	phosphate buffer	25 mM
7	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Designed protein TOP7	[U-15N; U-13C]	1 mM
9	phosphate buffer		25 mM
10	H2O		90 %
11	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
12	Designed protein TOP7	[U-15N]	1 mM
13	phosphate buffer		25 mM
14	H2O		90 %
15	D2O		10 %

4 3D 13C-filtered NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
1	Designed protein TOP7	1 mM
2	phosphate buffer	25 mM
3	H2O	90 %
4	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Concentration
5	Designed protein TOP7	1 mM
6	phosphate buffer	25 mM
7	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Designed protein TOP7	[U-15N; U-13C]	1 mM
9	phosphate buffer		25 mM
10	H2O		90 %
11	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
12	Designed protein TOP7	[U-15N]	1 mM
13	phosphate buffer		25 mM
14	H2O		90 %
15	D2O		10 %

nullKeywords Obligate symmetric homo-dimer

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Found 1 Document (1.703 seconds)

BMRB: 7101

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Designed protein TOP7, : 1 : 10 entities Detail

Experiments performed 4 experiments Detail

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