BMRB Entry 30097

Name: HDD domain from human Ddi2
Published: 2016-08-08

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PDB ID: 5k57
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30097
MolProbity Validation Chart

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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:

HDD domain from human Ddi2

Deposition date:

2016-05-23

Original release date:

2016-08-08

Authors:

Veverka, V.

Citation:

Citation: Siva, Monika; Svoboda, Michal; Veverka, Vaclav; Trempe, Jean-Francois; Hofmann, Kay; Kozisek, Milan; Hexnerova, Rozalie; Sedlak, Frantisek; Belza, Jan; Brynda, Jiri; Sacha, Pavel; Hubalek, Martin; Starkova, Jana; Flaisigova, Iva; Konvalinka, Jan; Saskova, Klara Grantz. "Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog" Sci. Rep. 6, 30443-30443 (2016).
PubMed: 27461074

Assembly members:

Assembly members:
Protein DDI1 homolog 2, polymer, 98 residues, 11130.358 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Protein DDI1 homolog 2: SQQSHSSPGEITSSPQGLDN PALLRDMLLANPHELSLLKE RNPPLAEALLSGDLEKFSRV LVEQQQDRARREQERIRLFS ADPFDLEAQAKIEEDIRQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	405
15N chemical shifts	103
1H chemical shifts	682

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 98 residues - 11130.358 Da.

1

SER

GLN

SER

HIS

SER

PRO

GLY

GLU

2

ILE

THR

SER

PRO

GLN

GLY

LEU

ASP

ASN

3

PRO

ALA

LEU

ARG

ASP

MET

LEU

ALA

4

ASN

PRO

HIS

GLU

LEU

SER

LEU

LYS

GLU

5

ARG

ASN

PRO

LEU

ALA

GLU

ALA

LEU

6

SER

GLY

ASP

LEU

GLU

LYS

PHE

SER

ARG

VAL

7

LEU

VAL

GLU

GLN

ASP

ARG

ALA

ARG

8

ARG

GLU

GLN

GLU

ARG

ILE

ARG

LEU

PHE

SER

9

ALA

ASP

PRO

PHE

ASP

LEU

GLU

ALA

GLN

ALA

10

LYS

ILE

GLU

ASP

ILE

ARG

GLN

Samples:

sample_1: hdd, [U-13C; U-15N], 280 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 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 HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection, processing

YASARA, Hoegenauer, Koraimann, Kungl, Vriend - refinement

NMR spectrometers:

Bruker AvanceIII 850 MHz
Bruker AvanceIII 600 MHz

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