BMRB Entry 16570

Name: NMR Structure of YbbR family protein Dhaf_0833 (residues 32-118) from Desulfitobacterium hafniense DCB-2: Northeast Structural Genomics Consortium target DhR29B
Published: 2012-01-24

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PDB ID: 2kpu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16570
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2009-10-20

Original release date:

2012-01-24

Authors:

Cort, John; Ramelot, Theresa; Yang, Yunhuang; Belote, Rachel; Ciccosanti, Colleen; Haleema, Janjua; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Barb, Adam; Cort, John; Seetharaman, Jayaraman; Lew, Scott; Lee, Hsiau-Wei; Acton, Thomas; Xiao, Rong; Kennedy, Michael; Tong, Liang; Montelione, Gaetano; Prestegard, James. "Structures of domains I and IV from YbbR are representative of a widely distributed protein family" Protein Sci. 20, 396-405 (2011).
PubMed: 21154411

Assembly members:

Assembly members:
Dhaf_0833, polymer, 96 residues, 10782 Da.

Natural source:

Natural source: Common Name: Desulfitobacterium hafniense Taxonomy ID: 49338 Superkingdom: Eubacteria Kingdom: not available Genus/species: Desulfitobacterium hafniense

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dhaf_0833: SSQTLDRDPTLTLSLIAKNT PANSMIMTKLPSVRVKTEGY NPSINVNELFAYVDLSGSEP GEHDYEVKVEPIPNIKIVEI SPRVVTLQLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	409
15N chemical shifts	94
1H chemical shifts	662

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Dhaf_0833	1

Entities:

Entity 1, Dhaf_0833 96 residues - 10782 Da.

1

SER

GLN

THR

LEU

ASP

ARG

ASP

PRO

THR

2

LEU

THR

LEU

SER

LEU

ILE

ALA

LYS

ASN

THR

3

PRO

ALA

ASN

SER

MET

ILE

MET

THR

LYS

LEU

4

PRO

SER

VAL

ARG

VAL

LYS

THR

GLU

GLY

TYR

5

ASN

PRO

SER

ILE

ASN

VAL

ASN

GLU

LEU

PHE

6

ALA

TYR

VAL

ASP

LEU

SER

GLY

SER

GLU

PRO

7

GLY

GLU

HIS

ASP

TYR

GLU

VAL

LYS

VAL

GLU

8

PRO

ILE

PRO

ASN

ILE

LYS

ILE

VAL

GLU

ILE

9

SER

PRO

ARG

VAL

THR

LEU

GLN

LEU

GLU

10

HIS

Samples:

sample_1: Dhaf_0833 (32-118), [U-100% 13C; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_2: Dhaf_0833 (32-118), [U-100% 13C; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; D2O 100%

sample_3: Dhaf_0833 (32-118), [5% 13C from 5% U-13C glucose in growth medium; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.23 M; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
4D 1H-13C-13C-1H HMQC-NOESY-HMQC	sample_2	isotropic	sample_conditions_1

Software:

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PSVS, Bhattacharya and Montelione - refinement

FELIX, Accelrys Software Inc. - processing

SPARKY, Goddard - data analysis, peak picking

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz
Bruker Avance 850 MHz

PDB	2KPU 2L5N 3LYW
GB	ACL18896
REF	WP_015943054