BMRB Entry 36136

Name: Designed protein dRafX6
Published: 2018-12-03

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PDB ID: 5yxi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR36136
MolProbity Validation Chart

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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:

Designed protein dRafX6

Deposition date:

2017-12-05

Original release date:

2018-12-03

Authors:

Liu, R.

Citation:

Citation: Liu, Ruicun; Wang, Jichao; Xiong, Peng; Chen, Quan; Liu, Haiyan. "De novo sequence redesign of a functional Ras-binding domain globally inverted the surface charge distribution and led to extreme thermostability" Biotechnol. Bioeng. 118, 2031-2042 (2021).
PubMed: 33590881

Assembly members:

Assembly members:
dRafX6, polymer, 79 residues, 8763.368 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
dRafX6: MADRTIEVELPNKQRTVINV RPGLTLKEALKKALKVRGID PNKVQVYLLLSGDDGAEQPL SLNHPAERLIGKKLKVVPL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	261
15N chemical shifts	69
1H chemical shifts	550

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 79 residues - 8763.368 Da.

1

MET

ALA

ASP

ARG

THR

ILE

GLU

VAL

GLU

LEU

2

PRO

ASN

LYS

GLN

ARG

THR

VAL

ILE

ASN

VAL

3

ARG

PRO

GLY

LEU

THR

LEU

LYS

GLU

ALA

LEU

4

LYS

ALA

LEU

LYS

VAL

ARG

GLY

ILE

ASP

5

PRO

ASN

LYS

VAL

GLN

VAL

TYR

LEU

6

SER

GLY

ASP

GLY

ALA

GLU

GLN

PRO

LEU

7

SER

LEU

ASN

HIS

PRO

ALA

GLU

ARG

LEU

ILE

8

GLY

LYS

LEU

LYS

VAL

PRO

LEU

Samples:

sample_1: dRafX6, [U-13C; U-15N], 0.5 mM; EDTA 0.01 mM; sodium phosphate 0.02 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 0.05 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert P., Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker DMX 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks