BMRB Entry 11328

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PDB ID: 2d8v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11328
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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 B-box domain of the zinc finger FYVE domain-containing protein 19 from Mus musculus

Deposition date:

2010-08-10

Original release date:

2011-08-19

Authors:

Miyamoto, K.; Kigawa, T.; Sato, M.; Koshiba, S.; Inoue, M.; Yokoyama, S.

Citation:

Citation: Miyamoto, K.; Kigawa, T.; Sato, M.; Koshiba, S.; Inoue, M.; Yokoyama, S.. "Solution structure of the B-box domain of the zinc finger FYVE domain-containing protein 19 from Mus musculus" .

Assembly members:

Assembly members:
zf-B box, polymer, 67 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: P050322-02

Entity Sequences (FASTA):

Entity Sequences (FASTA):
zf-B box: GSSGSSGLPWCCICNEDATL RCAGCDGDLYCARCFREGHD NFDLKEHQTSPYHPRRPCQE HSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	232
15N chemical shifts	53
1H chemical shifts	347

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	zf-B box	1
2	ZINC ION no.1	2
3	ZINC ION no.2	2

Entities:

Entity 1, zf-B box 67 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

LEU

PRO

TRP

2

CYS

ILE

CYS

ASN

GLU

ASP

ALA

THR

LEU

3

ARG

CYS

ALA

GLY

CYS

ASP

GLY

ASP

LEU

TYR

4

CYS

ALA

ARG

CYS

PHE

ARG

GLU

GLY

HIS

ASP

5

ASN

PHE

ASP

LEU

LYS

GLU

HIS

GLN

THR

SER

6

PRO

TYR

HIS

PRO

ARG

PRO

CYS

GLN

GLU

7

HIS

SER

GLY

PRO

SER

GLY

Entity 2, ZINC ION no.1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: zf-B_box, [U-13C; U-15N], 1.08 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; ZnCl2 0.05 mM; IDA 1.0 mM; H2O 90%; D2O 10%

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

Experiments:

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

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20031121, Delaglio, F. - processing

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

Kujira v0.9321, Kobayashi, N. - data analysis

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

NMR spectrometers:

Bruker AVANCE 900 MHz

PDB	2D8V
DBJ	BAB23993
GB	AAH18420 EDL27942 EDL27943
REF	NP_082330 XP_005603199 XP_006500266 XP_006500267 XP_006500268
SP	Q9DAZ9
AlphaFold	Q9DAZ9