BMRB Entry 10316

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PDB ID: 2dhk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10316
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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 PH domain of TBC1 domain family member 2 protein from human

Deposition date:

2009-03-11

Original release date:

2010-03-11

Authors:

Li, H.; Tochio, N.; Koshiba, S.; Harada, T.; Watanabe, S.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Li, H.; Tochio, N.; Koshiba, S.; Harada, T.; Watanabe, S.; Kigawa, T.; Yokoyama, S.. "Solution structure of the PH domain of TBC1 domain family member 2 protein from human" .

Assembly members:

Assembly members:
PH domain, polymer, 119 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: P051205-24

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PH domain: GSSGSSGKKLCGYLSKFGGK GPIRGWKSRWFFYDERKCQL YYSRTAQDANPLDSIDLSSA VFDCKADAEEGIFEIKTPSR VITLKAATKQAMLYWLQQLQ MKRWEFHNSPPAPSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	508
15N chemical shifts	110
1H chemical shifts	769

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PH domain	1

Entities:

Entity 1, PH domain 119 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

LYS

LEU

2

CYS

GLY

TYR

LEU

SER

LYS

PHE

GLY

LYS

3

GLY

PRO

ILE

ARG

GLY

TRP

LYS

SER

ARG

TRP

4

PHE

TYR

ASP

GLU

ARG

LYS

CYS

GLN

LEU

5

TYR

SER

ARG

THR

ALA

GLN

ASP

ALA

ASN

6

PRO

LEU

ASP

SER

ILE

ASP

LEU

SER

ALA

7

VAL

PHE

ASP

CYS

LYS

ALA

ASP

ALA

GLU

8

GLY

ILE

PHE

GLU

ILE

LYS

THR

PRO

SER

ARG

9

VAL

ILE

THR

LEU

LYS

ALA

THR

LYS

GLN

10

ALA

MET

LEU

TYR

TRP

LEU

GLN

LEU

GLN

11

MET

LYS

ARG

TRP

GLU

PHE

HIS

ASN

SER

PRO

12

PRO

ALA

PRO

SER

GLY

PRO

SER

GLY

Samples:

sample_1: PH domain, [U-13C; U-15N], 1.31 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: 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 v0.932, Kobayashi, N. - data analysis

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

NMR spectrometers:

Bruker AVANCE 900 MHz

PDB	2DHK
DBJ	BAD92958 BAG54761 BAH16625
EMBL	CAH92074
GB	AAK07684 AAL55877 EAW58882 EAW58883 EAW58884
REF	NP_001254500 NP_060891 XP_001158356 XP_003260594 XP_003260595
SP	Q9BYX2
AlphaFold	Q9BYX2