BMRB Entry 19710

Name: Solution structure of CDYL2 chromodomain
Published: 2014-04-22

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PDB ID: 2mj8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19710
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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 CDYL2 chromodomain

Deposition date:

2013-12-28

Original release date:

2014-04-22

Authors:

Qin, Su; Houliston, Scott; Arrowsmith, Cheryl; Edwards, Aled; Wu, Hong; Min, Jinrong

Citation:

Citation: Qin, Su; Houliston, Scott; Arrowsmith, Cheryl; Wu, Hong; Min, Jinrong. "Solution structure of CDYL2 chromodomain" .

Assembly members:

Assembly members:
entity, polymer, 64 residues, 7695.667 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28-MHL

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GASGDLYEVERIVDKRKNKK GKWEYLIRWKGYGSTEDTWE PEHHLLHCEEFIDEFNGLHM SKDK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	232
15N chemical shifts	54
1H chemical shifts	366

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CDYL2 chromodomain	1

Entities:

Entity 1, CDYL2 chromodomain 64 residues - 7695.667 Da.

1

GLY

ALA

SER

GLY

ASP

LEU

TYR

GLU

VAL

GLU

2

ARG

ILE

VAL

ASP

LYS

ARG

LYS

ASN

LYS

3

GLY

LYS

TRP

GLU

TYR

LEU

ILE

ARG

TRP

LYS

4

GLY

TYR

GLY

SER

THR

GLU

ASP

THR

TRP

GLU

5

PRO

GLU

HIS

LEU

HIS

CYS

GLU

6

PHE

ILE

ASP

GLU

PHE

ASN

GLY

LEU

HIS

MET

7

SER

LYS

ASP

LYS

Samples:

sample_1: TRIS 20 mM; sodium chloride 150 mM; DTT 2 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0.15 M; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

fmcgui v2.5, Lemak A. - chemical shift assignment, data analysis

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2MJ8 4HAE
DBJ	BAB29852 BAC04720 BAE24934 BAJ21089
GB	AAH58956 AAH69440 AAI00804 AAI00805 AAI00806
REF	NP_083717 NP_689555 XP_003791470 XP_004392121 XP_004690411
SP	Q8N8U2 Q9D5D8
AlphaFold	Q8N8U2 Q9D5D8