BMRB Entry 18391

Name: Solution structure of the R3H domain from human Smubp-2 in complex with 2&#039;-deoxyguanosine-5&#039;-monophosphate
Published: 2012-10-22

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PDB ID: 2lrr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18391
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 structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate

Deposition date:

2012-04-12

Original release date:

2012-10-22

Authors:

Jaudzems, Kristaps; Zhulenkovs, Dmitry; Otting, Gottfried; Liepinsh, Edvards

Citation:

Citation: Jaudzems, Kristaps; Jia, Xinying; Yagi, Hiromasa; Zhulenkovs, Dmitry; Graham, Bim; Otting, Gottfried; Liepinsh, Edvards. "Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2" J. Mol. Biol. 12, 760-767 (2012).
PubMed: 22999958

Assembly members:

Assembly members:
Smubp2_R3H, polymer, 86 residues, 8359.341 Da.
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, non-polymer, 347.221 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pQE60

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Smubp2_R3H: MGSLNGGSPEGVESQDGVDH FRAMIVEFMASKKMQLEFPP SLNSHDRLRVHQIAEEHGLR HDSSGEGKRRFITVSKRAGS HHHHHH

Data sets:

assigned_chemical_shifts

Data type	Count
15N chemical shifts	75
1H chemical shifts	921

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Smubp2_R3H	1
2	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	2

Entities:

Entity 1, Smubp2_R3H 86 residues - 8359.341 Da.

1

MET

GLY

SER

LEU

ASN

GLY

SER

PRO

GLU

2

GLY

VAL

GLU

SER

GLN

ASP

GLY

VAL

ASP

HIS

3

PHE

ARG

ALA

MET

ILE

VAL

GLU

PHE

MET

ALA

4

SER

LYS

MET

GLN

LEU

GLU

PHE

PRO

5

SER

LEU

ASN

SER

HIS

ASP

ARG

LEU

ARG

VAL

6

HIS

GLN

ILE

ALA

GLU

HIS

GLY

LEU

ARG

7

HIS

ASP

SER

GLY

GLU

GLY

LYS

ARG

8

PHE

ILE

THR

VAL

SER

LYS

ARG

ALA

GLY

SER

9

HIS

Entity 2, 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE - C10 H14 N5 O7 P - 347.221 Da.

1

DGP

Samples:

sample_1: Smubp2_R3H, [U-99% 15N], 0.9 ± 0.1 mM; 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 5.5 ± 0.1 mM; D2O, [U-100% 2H], 5 ± 0.1 %; sodium phosphate 10 ± 1 mM; sodium chloride 100 ± 5 mM; sodium azide 0.03 ± 0.005 %; H2O 95%

sample_conditions_1: ionic strength: 0.12 M; pH: 6.3; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1

Software:

VNMRJ v2.1b, Varian - collection

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

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

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

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

NMR spectrometers:

Varian INOVA 600 MHz

PDB	1MSZ 2LRR
DBJ	BAD92039 BAG35460
GB	AAA53082 AAA58611 AAA70430 AAH00290 AAH25299
REF	NP_002171 XP_002821469 XP_003274011 XP_003828806 XP_004051731
SP	P38935
AlphaFold	P38935