BMRB Entry 16578

Name: Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A.
Published: 2012-08-03

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PDB ID: 2kq2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16578
MolProbity Validation Chart

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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:

Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A.

Deposition date:

2009-10-24

Original release date:

2012-08-03

Authors:

Mills, Jeffrey; Eletsky, Alexander; Hua, Jia; Belote, Rachel; Buchwald, William; Ciccosanti, Colleen; Janjua, Haleema; Nair, R.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, Thomas

Citation:

Citation: Mills, Jeffrey; Eletsky, Alexander; Hua, Jia; Belote, Rachel; Buchwald, William; Ciccosanti, Colleen; Janjua, Haleema; Nair, R.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, Thomas. "Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A." .

Assembly members:

Assembly members:
DSY1790, polymer, 147 residues, 16692.779 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: pET 21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DSY1790: MDDRTEYDVYTDGSYVNGQY AWAYAFVKDGKVHYEDADVG KNPAAATMRNVAGEIAAALY AVKKASQLGVKIRILHDYAG IAFWATGEWKAKNEFTQAYA KLMNQYRGIYSFEKVKAHSG NEFNDYVDMKAKSALGIRDL EHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	394
15N chemical shifts	132
1H chemical shifts	838

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DSY1790	1

Entities:

Entity 1, DSY1790 147 residues - 16692.779 Da.

1

MET

ASP

ARG

THR

GLU

TYR

ASP

VAL

TYR

2

THR

ASP

GLY

SER

TYR

VAL

ASN

GLY

GLN

TYR

3

ALA

TRP

ALA

TYR

ALA

PHE

VAL

LYS

ASP

GLY

4

LYS

VAL

HIS

TYR

GLU

ASP

ALA

ASP

VAL

GLY

5

LYS

ASN

PRO

ALA

THR

MET

ARG

ASN

6

VAL

ALA

GLY

GLU

ILE

ALA

LEU

TYR

7

ALA

VAL

LYS

ALA

SER

GLN

LEU

GLY

VAL

8

LYS

ILE

ARG

ILE

LEU

HIS

ASP

TYR

ALA

GLY

9

ILE

ALA

PHE

TRP

ALA

THR

GLY

GLU

TRP

LYS

10

ALA

LYS

ASN

GLU

PHE

THR

GLN

ALA

TYR

ALA

11

LYS

LEU

MET

ASN

GLN

TYR

ARG

GLY

ILE

TYR

12

SER

PHE

GLU

LYS

VAL

LYS

ALA

HIS

SER

GLY

13

ASN

GLU

PHE

ASN

ASP

TYR

VAL

ASP

MET

LYS

14

ALA

LYS

SER

ALA

LEU

GLY

ILE

ARG

ASP

LEU

15

GLU

HIS

Samples:

NC: DhR1A, [U-99% 13C; U-99% 15N], 0.89 mM; D2O, [U-2H], 10 v/v; H2O 90 v/v; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02 w/v

NC5: DhR1A, [U-5% 13C; U-99% 15N], 0.943 mM; D2O, [U-2H], 10 v/v; H2O 90 v/v; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02 w/v

sample_conditions_1: ionic strength: 430 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC5	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC	isotropic	sample_conditions_1
3D HNCO	NC	isotropic	sample_conditions_1
3D HNCACB	NC	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC	isotropic	sample_conditions_1
3D HCCH-COSY	NC	isotropic	sample_conditions_1
3D simultaneous NOESY	NC	isotropic	sample_conditions_1

Software:

VNMRJ, Varian - collection

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

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

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

SPSCAN, Glaser - processing

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CSI, Wishart and Sykes - structure solution

TALOS, Cornilescu, Delaglio and Bax - structure solution

CYANA, Herrmann, Guntert and Wuthrich - structure solution

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

Molmol, Koradi, Billeter and Wuthrich - data analysis, refinement

PSVS, Bhattacharya and Montelione - refinement

NMR spectrometers:

Varian UnityPlus 600 MHz
Bruker Avance 800 MHz

BMRB	16807
PDB	2KQ2 2KW4
DBJ	BAE83579
EMBL	CDX01853
GB	ACL20967 EHL06967
REF	WP_005812143 WP_018211583 WP_019850577