BMRB Entry 18044

Name: Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds
Published: 2012-03-19

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PDB ID: 2lle
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18044
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds

Deposition date:

2011-11-07

Original release date:

2012-03-19

Authors:

Coles, Murray; Truffault, Vincent; Eisenbeis, Simone; Proffitt, William; Meiler, Jens; Hocker, Birte

Citation:

Citation: Eisenbeis, Simone; Proffitt, William; Coles, Murray; Truffault, Vincent; Shanmugarantam, Sooruban; Meiler, Jens; Hocker, Birte. "Potential of fragment recombination for rational design of proteins" J. Am. Chem. Soc. 134, 4019-4022 (2012).
PubMed: 22329686

Assembly members:

Assembly members:
CheYHisF-sfr_RM, polymer, 234 residues, 25607.779 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET 21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CheYHisF-sfr_RM: MGKIVLIVDDATNGREAVEK YKELKPDIVTMDITMPEMNG IDAIKEIMKIDPNAKIIVCS AMGQQAMVIEAIKAGAKGFI VNTAAVENPSLITQLAQTFG SQAVVVAIDAKRVDGEFMVF TYSGKKNTGILLRDWVVEVE KRGAGEILLTSIDRDGTKSG YDTEMIRFVRPLTTLPIIAS GGAGKMEHFLEAFLAGADAA AAASVFHFREIDGRELKEYL KKHGVNLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	904
15N chemical shifts	217
1H chemical shifts	1578

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CheYHisF-sfr_RM	1

Entities:

Entity 1, CheYHisF-sfr_RM 234 residues - 25607.779 Da.

The protein is an engineered chimera between CheY (1-11 and 34-103 from 1TMY) and HisF (103-247 from 1THF) from Thermotoga maritima with five point mutations (R4I, D78G, I95L, L201A, V213G). The last 7 residues represent a purification tag.

1

MET

GLY

LYS

ILE

VAL

LEU

ILE

VAL

ASP

2

ALA

THR

ASN

GLY

ARG

GLU

ALA

VAL

GLU

LYS

3

TYR

LYS

GLU

LEU

LYS

PRO

ASP

ILE

VAL

THR

4

MET

ASP

ILE

THR

MET

PRO

GLU

MET

ASN

GLY

5

ILE

ASP

ALA

ILE

LYS

GLU

ILE

MET

LYS

ILE

6

ASP

PRO

ASN

ALA

LYS

ILE

VAL

CYS

SER

7

ALA

MET

GLY

GLN

ALA

MET

VAL

ILE

GLU

8

ALA

ILE

LYS

ALA

GLY

ALA

LYS

GLY

PHE

ILE

9

VAL

ASN

THR

ALA

VAL

GLU

ASN

PRO

SER

10

LEU

ILE

THR

GLN

LEU

ALA

GLN

THR

PHE

GLY

11

SER

GLN

ALA

VAL

ALA

ILE

ASP

ALA

12

LYS

ARG

VAL

ASP

GLY

GLU

PHE

MET

VAL

PHE

13

THR

TYR

SER

GLY

LYS

ASN

THR

GLY

ILE

14

LEU

ARG

ASP

TRP

VAL

GLU

VAL

GLU

15

LYS

ARG

GLY

ALA

GLY

GLU

ILE

LEU

THR

16

SER

ILE

ASP

ARG

ASP

GLY

THR

LYS

SER

GLY

17

TYR

ASP

THR

GLU

MET

ILE

ARG

PHE

VAL

ARG

18

PRO

LEU

THR

LEU

PRO

ILE

ALA

SER

19

GLY

ALA

GLY

LYS

MET

GLU

HIS

PHE

LEU

20

GLU

ALA

PHE

LEU

ALA

GLY

ALA

ASP

ALA

21

ALA

SER

VAL

PHE

HIS

PHE

ARG

GLU

22

ILE

ASP

GLY

ARG

GLU

LEU

LYS

GLU

TYR

LEU

23

LYS

HIS

GLY

VAL

ASN

LEU

GLU

HIS

24

HIS

Samples:

15N-labelled: CheYHisF-sfr_RM, [U-100% 15N], 0.5 mM; potassium phosphate 50 mM; potassium chloride 300 mM; H2O 90%; D2O 10%

double-labelled: CheYHisF-sfr_RM, [U-100% 13C; U-100% 15N], 0.5 mM; potassium phosphate 50 mM; potassium chloride 300 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 350 mM; pH: 7.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	double-labelled	isotropic	sample_conditions_1
3D HNCA	double-labelled	isotropic	sample_conditions_1
3D HNCACB	double-labelled	isotropic	sample_conditions_1
3D C(CO)NH	double-labelled	isotropic	sample_conditions_1
3D CCH-TOCSY	double-labelled	isotropic	sample_conditions_1
3D CCH-COSY	double-labelled	isotropic	sample_conditions_1
2D PLUSH-TACSY	double-labelled	isotropic	sample_conditions_1
3D HNHA	15N-labelled	isotropic	sample_conditions_1
3D HNHB	15N-labelled	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N-labelled	isotropic	sample_conditions_1
3D 1H-13C NOESY	double-labelled	isotropic	sample_conditions_1
3D CNH-NOESY	double-labelled	isotropic	sample_conditions_1
3D CCH-NOESY	double-labelled	isotropic	sample_conditions_1
3D NNH-NOESY	15N-labelled	isotropic	sample_conditions_1
2D 15N-filtered 1H-1H NOESY	15N-labelled	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR NIH v2.21, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 800 MHz