BMRB Entry 16807

Name: Solution NMR Structure of the Holo Form of a Ribonuclease H domain from D.hafniense, Northeast Structural Genomics Consortium Target Target DhR1A
Published: 2010-04-14

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PDB ID: 2kw4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16807
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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 Holo Form of a Ribonuclease H domain from D.hafniense, Northeast Structural Genomics Consortium Target Target DhR1A

Deposition date:

2010-03-31

Original release date:

2010-04-14

Authors:

Mills, J.; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.

Citation:

Citation: Mills, Jeffrey; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.. "Northeast Structural Genomics Consortium Target DhR1A" To be published ., .-..

Assembly members:

Assembly members:
DhR1A, polymer, 147 residues, 16699.068 Da.
MG, non-polymer, 24.305 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: BL21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DhR1A: MDDRTEYDVYTDGSYVNGQY AWAYAFVKDGKVHYEDADVG KNPAAATMRNVAGEIAAALY AVKKASQLGVKIRILHDYAG IAFWATGEWKAKNEFTQAYA KLMNQYRGIYSFEKVKAHSG NEFNDYVDMKAKSALGIRDL EHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list
- Cpeaks
- Npeaks

Data type	Count
13C chemical shifts	372
15N chemical shifts	134
1H chemical shifts	821

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DhR1A	1
2	Magnesium ion	2

Entities:

Entity 1, DhR1A 147 residues - 16699.068 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

Entity 2, Magnesium ion - Mg - 24.305 Da.

1

MG

Samples:

sample: DhR1A, [U-100% 13C; U-100% 15N], 0.89 mM; MAGNESIUM Chloride 150 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample	isotropic	sample_conditions_1
3D HNCO	sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample	isotropic	sample_conditions_1
3D HNCACB	sample	isotropic	sample_conditions_1
3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY	sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample	isotropic	sample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - geometry optimization, refinement, structure solution

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

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

TOPSPIN, Bruker Biospin - collection

VNMRJ, Varian - collection

CARA, Keller and Wuthrich - chemical shift assignment

Molmol, Koradi, Billeter and Wuthrich - refinement

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 900 MHz
Varian INOVA 750 MHz

BMRB	16578
PDB	2KQ2 2KW4
DBJ	BAE83579
EMBL	CDX01853
GB	ACL20967 EHL06967
REF	WP_005812143 WP_018211583 WP_019850577