BMRB Entry 16577

Name: Backbone Chemical Shift Assignments of Mouse HOXA13 DNA Binding Domain in Complex with DNA Duplex
Published: 2010-03-24

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PDB ID: 2ld5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16577
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone Chemical Shift Assignments of Mouse HOXA13 DNA Binding Domain in Complex with DNA Duplex

Deposition date:

2009-10-23

Original release date:

2010-03-24

Authors:

Zhang, Yonghong

Citation:

Citation: Zhang, Yonghong; Thornburg, Chelsea; Stadler, H. Scott; Ames, James. "Backbone chemical shift assignments of mouse HOXA13 DNA binding domain bound to duplex DNA." Biomol. NMR Assignments 4, 97-99 (2010).
PubMed: 20232265

Assembly members:

Assembly members:
DNA_duplex_chain_1, polymer, 11 residues, Formula weight is not available
DNA_duplex_chain_2, polymer, 11 residues, Formula weight is not available
Hoxa13_DNA_binding_domain, polymer, 73 residues, 8792 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_duplex_chain_1: CAAATAAAATC
DNA_duplex_chain_2: GATTTTATTTG
Hoxa13_DNA_binding_domain: GSHMLEGRKKRVPYTKVQLK ELEREYATNKFITKDKRRRI SATTNLSERQVTIWFQNRRV KEKKVINKLKTTS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	211
15N chemical shifts	70
1H chemical shifts	142

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA duplex, chain 1	1
2	DNA duplex, chain 2	2
3	Hoxa13 DNA binding domain	3

Entities:

Entity 1, DNA duplex, chain 1 11 residues - Formula weight is not available

1

DC

DA

DT

DA

DT

2

DC

Entity 2, DNA duplex, chain 2 11 residues - Formula weight is not available

1

DG

DA

DT

DA

DT

2

DG

Entity 3, Hoxa13 DNA binding domain 73 residues - 8792 Da.

1

GLY

SER

HIS

MET

LEU

GLU

GLY

ARG

LYS

2

ARG

VAL

PRO

TYR

THR

LYS

VAL

GLN

LEU

LYS

3

GLU

LEU

GLU

ARG

GLU

TYR

ALA

THR

ASN

LYS

4

PHE

ILE

THR

LYS

ASP

LYS

ARG

ILE

5

SER

ALA

THR

ASN

LEU

SER

GLU

ARG

GLN

6

VAL

THR

ILE

TRP

PHE

GLN

ASN

ARG

VAL

7

LYS

GLU

LYS

VAL

ILE

ASN

LYS

LEU

LYS

8

THR

SER

Samples:

sample_1: DNA duplex, chain 1 0.5 mM; DNA duplex, chain 2 0.5 mM; Hoxa13 DNA binding domain, [U-98% 13C; U-98% 15N], 0.5 mM; sodium phosphate 20 mM; magnesium chloride 5 mM

sample_2: DNA duplex, chain 1 0.5 mM; DNA duplex, chain 2 0.5 mM; Hoxa13 DNA binding domain, [U-98% 13C; U-98% 15N], 0.5 mM; sodium phosphate 20 mM; magnesium chloride 5 mM

sample_conditions_1: ionic strength: 0.025 M; pH: 6.0; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

NMR spectrometers:

Bruker Avance 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks