BMRB Entry 10296

Name: Solution structure of the homeobox domain of Homeobox protein goosecoid
Published: 2009-12-17

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PDB ID: 2dmu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR10296
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 homeobox domain of Homeobox protein goosecoid

Deposition date:

2008-12-17

Original release date:

2009-12-17

Authors:

Ohnishi, S.; Sato, M.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Ohnishi, S.; Sato, M.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.. "Solution structure of the homeobox domain of Homeobox protein goosecoid" .

Assembly members:

Assembly members:
homeobox domain, polymer, 70 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: cell free synthesis Vector: P050919-23

Entity Sequences (FASTA):

Entity Sequences (FASTA):
homeobox domain: GSSGSSGRRHRTIFTDEQLE ALENLFQETKYPDVGTREQL ARKVHLREEKVEVWFKNRRA KWRRSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	280
15N chemical shifts	63
1H chemical shifts	423

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	homeobox domain	1

Entities:

Entity 1, homeobox domain 70 residues - Formula weight is not available

1	GLY	SER	SER	GLY	SER	SER	GLY	ARG	ARG	HIS
2	ARG	THR	ILE	PHE	THR	ASP	GLU	GLN	LEU	GLU
3	ALA	LEU	GLU	ASN	LEU	PHE	GLN	GLU	THR	LYS
4	TYR	PRO	ASP	VAL	GLY	THR	ARG	GLU	GLN	LEU
5	ALA	ARG	LYS	VAL	HIS	LEU	ARG	GLU	GLU	LYS
6	VAL	GLU	VAL	TRP	PHE	LYS	ASN	ARG	ARG	ALA
7	LYS	TRP	ARG	ARG	SER	GLY	PRO	SER	SER	GLY

Samples:

sample_1: homeobox domain, [U-13C; U-15N], 1.3 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; D2O 10%; H2O 90%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	isotropic	condition_1
3D 15N-separated NOESY	sample_1	isotropic	condition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20030801, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.965, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, P. - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 700 MHz

PDB	2DMU
DBJ	BAG73208 BAK40073 BAR79454
EMBL	CAA49897 CAA73611 CAA73612 CAA76833 CAJ82436
GB	AAA37826 AAA49729 AAA49744 AAA50028 AAA50030
REF	NP_001016704 NP_001074955 NP_001081278 NP_001093429 NP_001107361
SP	A1YEY5 A1YFI3 A1YG57 A2T733 A2T7P4
TPG	DAA17416
AlphaFold	A1YEY5 A1YFI3 A1YG57 A2T733 A2T7P4

1	GLY	SER	SER	GLY	SER	SER	GLY	ARG	ARG	HIS
2	ARG	THR	ILE	PHE	THR	ASP	GLU	GLN	LEU	GLU
3	ALA	LEU	GLU	ASN	LEU	PHE	GLN	GLU	THR	LYS
4	TYR	PRO	ASP	VAL	GLY	THR	ARG	GLU	GLN	LEU
5	ALA	ARG	LYS	VAL	HIS	LEU	ARG	GLU	GLU	LYS
6	VAL	GLU	VAL	TRP	PHE	LYS	ASN	ARG	ARG	ALA
7	LYS	TRP	ARG	ARG	SER	GLY	PRO	SER	SER	GLY

1	GLY	SER	SER	GLY	SER	SER	GLY	ARG	ARG	HIS
2	ARG	THR	ILE	PHE	THR	ASP	GLU	GLN	LEU	GLU
3	ALA	LEU	GLU	ASN	LEU	PHE	GLN	GLU	THR	LYS
4	TYR	PRO	ASP	VAL	GLY	THR	ARG	GLU	GLN	LEU
5	ALA	ARG	LYS	VAL	HIS	LEU	ARG	GLU	GLU	LYS
6	VAL	GLU	VAL	TRP	PHE	LYS	ASN	ARG	ARG	ALA
7	LYS	TRP	ARG	ARG	SER	GLY	PRO	SER	SER	GLY