BMRB Entry 30102

Name: Solution structure of the yeast Ddi1 HDD domain
Published: 2016-09-30

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PDB ID: 5kes
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30102
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: Solution structure of the yeast Ddi1 HDD domain PubMed: 27646017

Deposition date: 2016-06-10 Original release date: 2016-09-30

Authors: Trempe, J.-F.; Ratcliffe, C.; Veverka, V.; Saskova, K.; Gehring, K.

Citation: Trempe, J.; Saskova, K.; Siva, M.; Ratcliffe, C.; Veverka, V.; Hoegl, A.; Menade, M.; Feng, X.; Shenker, S.; Svoboda, M.; Kozisek, M.; Konvalinka, J.; Gehring, K.. "Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family." Sci. Rep. 6, 33671-33671 (2016).

Assembly members:
entity_1, polymer, 116 residues, 13309.941 Da.

Natural source: Common Name: Baker's yeast Taxonomy ID: 559292 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source: Production method: recombinant technology Host organism: Escherichia coli K-12

Entity Sequences (FASTA):
entity_1: GPLGSATLSDEAFIEQFRQE LLNNQMLRSQLILQIPGLND LVNDPLLFRERLGPLILQRR YGGYNTAMNPFGIPQDEYTR LMANPDDPDNKKRIAELLDQ QAIDEQLRNAIEYTPE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	507
15N chemical shifts	126
1H chemical shifts	857

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_1 116 residues - 13309.941 Da.

1

GLY

PRO

LEU

GLY

SER

ALA

THR

LEU

SER

ASP

2

GLU

ALA

PHE

ILE

GLU

GLN

PHE

ARG

GLN

GLU

3

LEU

ASN

GLN

MET

LEU

ARG

SER

GLN

4

LEU

ILE

LEU

GLN

ILE

PRO

GLY

LEU

ASN

ASP

5

LEU

VAL

ASN

ASP

PRO

LEU

PHE

ARG

GLU

6

ARG

LEU

GLY

PRO

LEU

ILE

LEU

GLN

ARG

7

TYR

GLY

TYR

ASN

THR

ALA

MET

ASN

PRO

8

PHE

GLY

ILE

PRO

GLN

ASP

GLU

TYR

THR

ARG

9

LEU

MET

ALA

ASN

PRO

ASP

PRO

ASP

ASN

10

LYS

ARG

ILE

ALA

GLU

LEU

ASP

GLN

11

GLN

ALA

ILE

ASP

GLU

GLN

LEU

ARG

ASN

ALA

12

ILE

GLU

TYR

THR

PRO

GLU

Samples:

sample_1: Ddi1 86-196-1, [U-13C; U-15N], 0.5 ± 0.1 mM

sample_2: Ddi1 86-196-2, [U-15N], 0.5 ± 0.1 mM

sample_conditions_1: ionic strength: 110 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 110 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N het NOE	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC-IPAP	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC-IPAP	sample_2	anisotropic	sample_conditions_2
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 15N/1H NOESY-HSQC	sample_1	isotropic	sample_conditions_1
3D 13C/1H HSQC-NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

MODULE, M. Blackledge - data analysis

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

XPLOR-NIH v2.40, C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore - refinement, structure calculation

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 850 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts