BMRB Entry 11347

Name: Solution structure of the PHD domain in PHD finger protein 21A
Published: 2011-09-07

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PDB ID: 2yql
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11347
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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 PHD domain in PHD finger protein 21A

Deposition date:

2010-09-07

Original release date:

2011-09-07

Authors:

He, F.; Muto, Y.; Inoue, M.; Kigawa, T.; Shirouzu, M.; Terada, T.; Yokoyama, S.

Citation:

Citation: He, F.; Muto, Y.; Inoue, M.; Kigawa, T.; Shirouzu, M.; Terada, T.; Yokoyama, S.. "Solution structure of the PHD domain in PHD finger protein 21A" .

Assembly members:

Assembly members:
PHD domain, polymer, 56 residues, Formula weight is not available
ZN, non-polymer, 65.409 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: cell free synthesis Host organism: E. coli - cell free Vector: P061030-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PHD domain: GSSGSSGHEDFCSVCRKSGQ LLMCDTCSRVYHLDCLDPPL KTIPKGMWICPRCQDQ

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	224
15N chemical shifts	50
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	PHD domain	1
2	ZINC ION no.1	2
3	ZINC ION no.2	2

Entities:

Entity 1, PHD domain 56 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

HIS

GLU

ASP

2

PHE

CYS

SER

VAL

CYS

ARG

LYS

SER

GLY

GLN

3

LEU

MET

CYS

ASP

THR

CYS

SER

ARG

VAL

4

TYR

HIS

LEU

ASP

CYS

LEU

ASP

PRO

LEU

5

LYS

THR

ILE

PRO

LYS

GLY

MET

TRP

ILE

CYS

6

PRO

ARG

CYS

GLN

ASP

GLN

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

1

ZN

Samples:

sample_1: PHD domain, [U-13C; U-15N], 1.0 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 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 v0.9820, Kobayashi, N. - data analysis

CYANA v2.1, Guntert, P. - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz

PDB	2PUY 2YQL
DBJ	BAB14492 BAB21787 BAC29735 BAC65327 BAC98234
EMBL	CAH10542 CDQ58507
GB	AAF64262 AAH15714 AAH19181 AAM09095 ABZ92334
REF	NP_001095272 NP_001103160 NP_001103161 NP_001186576 NP_001193126
SP	Q6ZPK0 Q96BD5
TPG	DAA21793 DAA21794
AlphaFold	Q6ZPK0 Q96BD5