BMRB Entry 11237

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PDB ID: 2ysm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11237
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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 first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog

Deposition date:

2010-07-23

Original release date:

2011-08-03

Authors:

Qin, X.; Hayashi, F.; Yokoyama, S.

Citation:

Citation: Qin, X.; Hayashi, F.; Yokoyama, S.. "Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog" .

Assembly members:

Assembly members:
PHD domain, polymer, 111 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: P070115-52

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PHD domain: GSSGSSGANCAVCDSPGDLL DQFFCTTCGQHYHGMCLDIA VTPLKRAGWQCPECKVCQNC KQSGEDSKMLVCDTCDKGYH TFCLQPVMKSVPTNGWKCKN CRICISGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	454
15N chemical shifts	113
1H chemical shifts	699

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
4	ZINC ION no.3	2
5	ZINC ION no.4	2

Entities:

Entity 1, PHD domain 111 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

ALA

ASN

CYS

2

ALA

VAL

CYS

ASP

SER

PRO

GLY

ASP

LEU

3

ASP

GLN

PHE

CYS

THR

CYS

GLY

GLN

4

HIS

TYR

HIS

GLY

MET

CYS

LEU

ASP

ILE

ALA

5

VAL

THR

PRO

LEU

LYS

ARG

ALA

GLY

TRP

GLN

6

CYS

PRO

GLU

CYS

LYS

VAL

CYS

GLN

ASN

CYS

7

LYS

GLN

SER

GLY

GLU

ASP

SER

LYS

MET

LEU

8

VAL

CYS

ASP

THR

CYS

ASP

LYS

GLY

TYR

HIS

9

THR

PHE

CYS

LEU

GLN

PRO

VAL

MET

LYS

SER

10

VAL

PRO

THR

ASN

GLY

TRP

LYS

CYS

LYS

ASN

11

CYS

ARG

ILE

CYS

ILE

SER

GLY

PRO

SER

12

GLY

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

1

ZN

Samples:

sample_1: PHD domain, [U-13C; U-15N], 0.94 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; ZnCl2 0.05 mM; IDA 1 mM; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 293 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:

VNMR v6.1C, Varian - collection

NMRPipe v20030801, Delaglio, F. - processing

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

Kujira v0.9820, Kobayashi, N. - data analysis

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

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 900 MHz

PDB	2YSM
DBJ	BAC35712
REF	XP_007948343 XP_010639685 XP_010639691 XP_010639698