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BMRB: 16570

2KPU

NMR Structure of YbbR family protein Dhaf_0833 (residues 32-118) from Desulfitobacterium hafniense DCB-2: Northeast Structural Genomics Consortium target DhR29B

Authors

Cort, J.R., Ramelot, T.A., Yang, Y., Belote, R.L., Ciccosanti, C., Haleema, J., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A.

Assembly

YbbR family protein Dhaf 0833

Entity

1. YbbR family protein Dhaf 0833 (polymer, Thiol state: not present), 96 monomers, 10776.06 Da Detail

SSQTLDRDPT LTLSLIAKNT PANSMIMTKL PSVRVKTEGY NPSINVNELF AYVDLSGSEP GEHDYEVKVE PIPNIKIVEI SPRVVTLQLE HHHHHH

Formula weight

10776.06 Da

Source organism

Desulfitobacterium hafniense

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 91.3 %, Completeness (bb): 93.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1016 of 1113)	91.9 % (530 of 577)	89.8 % (395 of 440)	94.8 % (91 of 96)
Backbone	93.0 % (521 of 560)	94.1 % (176 of 187)	91.9 % (262 of 285)	94.3 % (83 of 88)
Sidechain	90.2 % (583 of 646)	90.8 % (354 of 390)	89.1 % (221 of 248)	100.0 % (8 of 8)
Aromatic	32.3 % (20 of 62)	32.3 % (10 of 31)	32.3 % (10 of 31)
Methyl	97.5 % (117 of 120)	96.7 % (58 of 60)	98.3 % (59 of 60)

1. Dhaf 0833

SSQTLDRDPT LTLSLIAKNT PANSMIMTKL PSVRVKTEGY NPSINVNELF AYVDLSGSEP GEHDYEVKVE PIPNIKIVEI SPRVVTLQLE HHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Dhaf_0833 (32-118)	[U-100% 13C; U-100% 15N]	0.8 mM
2	ammonium acetate	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	calcium chloride	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
8	Dhaf_0833 (32-118)	[U-100% 13C; U-100% 15N]	0.8 mM
9	ammonium acetate	natural abundance	20 mM
10	sodium chloride	natural abundance	200 mM
11	calcium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	0.02 %
13	D2O	natural abundance	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
14	Dhaf_0833 (32-118)	[5% 13C from 5% U-13C glucose in growth medium; U-100% 15N]	0.8 mM
15	ammonium acetate	natural abundance	20 mM
16	sodium chloride	natural abundance	200 mM
17	calcium chloride	natural abundance	10 mM
18	sodium azide	natural abundance	0.02 %
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

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: -0.04 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: -0.04 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: 0.02 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: 0.68 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2012-01-23

Citation

Structures of domains I and IV from YbbR are representative of a widely distributed protein family
Barb, A.W., Cort, J.R., Seetharaman, J., Lew, S., Lee, H., Acton, T., Xiao, R., Kennedy, M.A., Tong, L., Montelione, G.T., Prestegard, J.H.
Protein Sci. (2011), 20, 396-405, PubMed 21154411 , DOI 10.1002/pro.571 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 16576 released on 2010-01-06
    Title Solution Structure Of Protein BH0266 From Bacillus halodurans. Northeast Structural Genomics Consortium Target BhR97a
  BMRB: 16568 released on 2009-11-03
    Title Solution Structure of Domain IV from the YbbR family protein of Desulfitobacterium hafniense

Related entities 1. YbbR family protein Dhaf 0833, : 1 : 1 : 1 : 2 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC