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BMRB: 16272

2KIF

Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.

Authors

Aramini, J.M., Belote, R.L., Ciccosanti, C.T., Jiang, M., Rost, B., Nair, R., Swapna, G.VT., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T.

Assembly

VpR247

Entity

1. VpR247 (polymer, Thiol state: not present), 108 monomers, 12316.11 Da Detail

MDQFLVQIFA VIHQIPKGKV STYGEIAKMA GYPGYARHVG KALGNLPEGS KLPWFRVINS QGKISLKGRD LDRQKQKLEA EGIEVSEIGK IALRKYKWQP LEHHHHHH

Formula weight

12316.11 Da

Source organism

Vibrio parahaemolyticus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 93.1 %, Completeness (bb): 92.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.1 % (1231 of 1322)	93.3 % (650 of 697)	93.3 % (477 of 511)	91.2 % (104 of 114)
Backbone	92.0 % (587 of 638)	91.4 % (203 of 222)	93.0 % (291 of 313)	90.3 % (93 of 103)
Sidechain	94.1 % (735 of 781)	94.1 % (447 of 475)	93.9 % (277 of 295)	100.0 % (11 of 11)
Aromatic	79.7 % (94 of 118)	79.7 % (47 of 59)	78.9 % (45 of 57)	100.0 % (2 of 2)
Methyl	100.0 % (112 of 112)	100.0 % (56 of 56)	100.0 % (56 of 56)

1. VpR247

MDQFLVQIFA VIHQIPKGKV STYGEIAKMA GYPGYARHVG KALGNLPEGS KLPWFRVINS QGKISLKGRD LDRQKQKLEA EGIEVSEIGK IALRKYKWQP LEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 5-mm Shigemi

#	Name	Isotope labeling	Concentration
1	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	DSS	natural abundance	50 uM
8	H20	natural abundance	90 %
9	D20	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 1.7-mm microtube

#	Name	Isotope labeling	Concentration
10	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
11	MES	natural abundance	20 mM
12	sodium chloride	natural abundance	200 mM
13	calcium chloride	natural abundance	5 mM
14	DTT	natural abundance	10 mM
15	sodium azide	natural abundance	0.02 %
16	DSS	natural abundance	50 uM
17	H20	natural abundance	90 %
18	D20	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 1.7-mm microtube

#	Name	Isotope labeling	Concentration
19	VpR247	[U-5% 13C; U-100% 15N]	0.92 mM
20	MES	natural abundance	20 mM
21	sodium chloride	natural abundance	200 mM
22	calcium chloride	natural abundance	5 mM
23	DTT	natural abundance	10 mM
24	sodium azide	natural abundance	0.02 %
25	DSS	natural abundance	50 uM
26	H20	natural abundance	90 %
27	D20	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.07 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-03-08

Citation

Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247
Aramini, J.M., Belote, R.L., Ciccosanti, C.T., Jiang, M., Rost, B., Nair, R., Swapna, G.VT., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T.
Not known

Related entities 1. VpR247, : 1 : 1 : 1 : 23 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz 5-mm TXI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 5-mm Shigemi

#	Name	Isotope labeling	Concentration
1	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	DSS	natural abundance	50 uM
8	H20	natural abundance	90 %
9	D20	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz 5-mm TXI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 5-mm Shigemi

#	Name	Isotope labeling	Concentration
1	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	DSS	natural abundance	50 uM
8	H20	natural abundance	90 %
9	D20	natural abundance	10 %

3 3D simultaneous CN NOESY

Instrument

Bruker Avance - 800 MHz 5-mm TXI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 5-mm Shigemi

#	Name	Isotope labeling	Concentration
1	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	DSS	natural abundance	50 uM
8	H20	natural abundance	90 %
9	D20	natural abundance	10 %

4 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz 5-mm TXI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5, Details 5-mm Shigemi

#	Name	Isotope labeling	Concentration
1	VpR247	[U-100% 13C; U-100% 15N]	0.94 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	DSS	natural abundance	50 uM
8	H20	natural abundance	90 %
9	D20	natural abundance	10 %

5 3D HNCO