BMRB Entry 34489

Name: Designing a Granulopoietic Protein by Topological Rescaffolding 1: Sohair
Published: 2020-03-16

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PDB ID: 6y07
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34489
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:

Designing a Granulopoietic Protein by Topological Rescaffolding 1: Sohair

Deposition date:

2020-02-06

Original release date:

2020-03-16

Authors:

ElGamacy, M.; Coles, M.

Citation:

Citation: Alvarez, Birte; Skokowa, Julia; Coles, Murray; Mir, Perihan; Nasri, Masoud; Maksymenko, Kateryna; Weidmann, Laura; Rogers, Katherine; Welte, Karl; Lupas, Andrei; Muller, Patrick; ElGamacy, Mohammad. "Design of novel granulopoietic proteins by topological rescaffolding" PLoS Biol. 18, e3000919-e3000919 (2020).
PubMed: 33351791

Assembly members:

Assembly members:
entity_1, polymer, 175 residues, 20297.090 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):
entity_1: MGSSHHHHHHSSGLVPRGSH MMTSDYIIEQIQRKQEEARL KVEEMERKLEAVKEASKRGV SSDQLLNLILDLADIITTLI QIIEESNEAIKELIKNQKGP TSDYIIEQIQRDQEEARKKV EEAEERLERVKEASKRGVSS DQLLDLIRELAEIIEELIRI IRRSNEAIKELIKNQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	644
15N chemical shifts	159
1H chemical shifts	531

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_1 175 residues - 20297.090 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

THR

SER

ASP

TYR

ILE

GLU

GLN

4

ILE

GLN

ARG

LYS

GLN

GLU

ALA

ARG

LEU

5

LYS

VAL

GLU

MET

GLU

ARG

LYS

LEU

GLU

6

ALA

VAL

LYS

GLU

ALA

SER

LYS

ARG

GLY

VAL

7

SER

ASP

GLN

LEU

ASN

LEU

ILE

LEU

8

ASP

LEU

ALA

ASP

ILE

THR

LEU

ILE

9

GLN

ILE

GLU

SER

ASN

GLU

ALA

ILE

10

LYS

GLU

LEU

ILE

LYS

ASN

GLN

LYS

GLY

PRO

11

THR

SER

ASP

TYR

ILE

GLU

GLN

ILE

GLN

12

ARG

ASP

GLN

GLU

ALA

ARG

LYS

VAL

13

GLU

ALA

GLU

ARG

LEU

GLU

ARG

VAL

14

LYS

GLU

ALA

SER

LYS

ARG

GLY

VAL

SER

15

ASP

GLN

LEU

ASP

LEU

ILE

ARG

GLU

LEU

16

ALA

GLU

ILE

GLU

LEU

ILE

ARG

ILE

17

ILE

ARG

SER

ASN

GLU

ALA

ILE

LYS

GLU

18

LEU

ILE

LYS

ASN

GLN

Samples:

sample_1: sohair, [U-99% 13C; U-99% 15N], 650 uM; PBS 50 mM

sample_conditions_1: ionic strength: 125 mM; pH: 5.2; pressure: 1 atm; temperature: 315 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D (H)CC(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
3D CNH-NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D NNH-NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - data analysis

Sparky, Goddard - chemical shift assignment

Rosetta, Baker - structure calculation

CoMAND, in house - refinement

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz

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