BMRB Entry 26641

Name: Backbone assignments for E. coli MurD
Published: 2015-12-17

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26641

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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:

Backbone assignments for E. coli MurD

Deposition date:

2015-08-27

Original release date:

2015-12-17

Authors:

Ogura, Kenji; Kumeta, Hiroyuki; Yokochi, Masashi; Inagaki, Fuyuhiko

Citation:

Citation: Saio, Tomohide; Ogura, Kenji; Kumeta, Hiroyuki; Kobashigawa, Yoshihiro; Shimizu, Kazumi; Yokochi, Masashi; Kodama, Kota; Yamaguchi, Hiroto; Tsujishita, Hideki; Inagaki, Fuyuhiko. "Ligand-driven conformational changes of MurD visualized by paramagnetic NMR" Sci. Rep. ., .-. (2015).
PubMed: 2015

Assembly members:

Assembly members:
MurD, polymer, 441 residues, Formula weight is not available

Natural source:

Natural source: Common Name: enterobacteria 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: pGBHPS

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MurD: HMGSADYQGKNVVIIGLGLT GLSCVDFFLARGVTPRVMDT RMTPPGLDKLPEAVERHTGS LNDEWLMAADLIVASPGIAL AHPSLSAAADAGIEIVGDIE LFCREAQAPIVAITGSNGKS TVTTLVGEMAKAAGVNVGVG GNIGLPALMLLDDECELYVL ELSSFQLETTSSLQAVAATI LNVTEDHMDRYPFGLQQYRA AKLRIYENAKVCVVNADDAL TMPIRGADERCVSFGVNMGD YHLNHQQGETWLRVKGEKVL NVKEMKLSGQHNYTNALAAL ALADAAGLPRASSLKALTTF TGLPHRFEVVLEHNGVRWIN DSKATNVGSTEAALNGLHVD GTLHLLLGGDGKSADFSPLA RYLNGDNVRLYCFGRDGAQL AALRPEVAEQTETMEQAMRL LAPRVQPGDMVLLSPACASL DQFKNFEQRGNEFARLAKEL G

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	371
1H chemical shifts	371

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MurD monomer	1

Entities:

Entity 1, MurD monomer 441 residues - Formula weight is not available

"HMGS" at the N-terminus is cloning artifact. Ala right after "HMGS" is the first residue.

1

HIS

MET

GLY

SER

ALA

ASP

TYR

GLN

GLY

LYS

2

ASN

VAL

ILE

GLY

LEU

GLY

LEU

THR

3

GLY

LEU

SER

CYS

VAL

ASP

PHE

LEU

ALA

4

ARG

GLY

VAL

THR

PRO

ARG

VAL

MET

ASP

THR

5

ARG

MET

THR

PRO

GLY

LEU

ASP

LYS

LEU

6

PRO

GLU

ALA

VAL

GLU

ARG

HIS

THR

GLY

SER

7

LEU

ASN

ASP

GLU

TRP

LEU

MET

ALA

ASP

8

LEU

ILE

VAL

ALA

SER

PRO

GLY

ILE

ALA

LEU

9

ALA

HIS

PRO

SER

LEU

SER

ALA

ASP

10

ALA

GLY

ILE

GLU

ILE

VAL

GLY

ASP

ILE

GLU

11

LEU

PHE

CYS

ARG

GLU

ALA

GLN

ALA

PRO

ILE

12

VAL

ALA

ILE

THR

GLY

SER

ASN

GLY

LYS

SER

13

THR

VAL

THR

LEU

VAL

GLY

GLU

MET

ALA

14

LYS

ALA

GLY

VAL

ASN

VAL

GLY

VAL

GLY

15

GLY

ASN

ILE

GLY

LEU

PRO

ALA

LEU

MET

LEU

16

LEU

ASP

GLU

CYS

GLU

LEU

TYR

VAL

LEU

17

GLU

LEU

SER

PHE

GLN

LEU

GLU

THR

18

SER

LEU

GLN

ALA

VAL

ALA

THR

ILE

19

LEU

ASN

VAL

THR

GLU

ASP

HIS

MET

ASP

ARG

20

TYR

PRO

PHE

GLY

LEU

GLN

TYR

ARG

ALA

21

ALA

LYS

LEU

ARG

ILE

TYR

GLU

ASN

ALA

LYS

22

VAL

CYS

VAL

ASN

ALA

ASP

ALA

LEU

23

THR

MET

PRO

ILE

ARG

GLY

ALA

ASP

GLU

ARG

24

CYS

VAL

SER

PHE

GLY

VAL

ASN

MET

GLY

ASP

25

TYR

HIS

LEU

ASN

HIS

GLN

GLY

GLU

THR

26

TRP

LEU

ARG

VAL

LYS

GLY

GLU

LYS

VAL

LEU

27

ASN

VAL

LYS

GLU

MET

LYS

LEU

SER

GLY

GLN

28

HIS

ASN

TYR

THR

ASN

ALA

LEU

ALA

LEU

29

ALA

LEU

ALA

ASP

ALA

GLY

LEU

PRO

ARG

30

ALA

SER

LEU

LYS

ALA

LEU

THR

PHE

31

THR

GLY

LEU

PRO

HIS

ARG

PHE

GLU

VAL

32

LEU

GLU

HIS

ASN

GLY

VAL

ARG

TRP

ILE

ASN

33

ASP

SER

LYS

ALA

THR

ASN

VAL

GLY

SER

THR

34

GLU

ALA

LEU

ASN

GLY

LEU

HIS

VAL

ASP

35

GLY

THR

LEU

HIS

LEU

GLY

ASP

36

GLY

LYS

SER

ALA

ASP

PHE

SER

PRO

LEU

ALA

37

ARG

TYR

LEU

ASN

GLY

ASP

ASN

VAL

ARG

LEU

38

TYR

CYS

PHE

GLY

ARG

ASP

GLY

ALA

GLN

LEU

39

ALA

LEU

ARG

PRO

GLU

VAL

ALA

GLU

GLN

40

THR

GLU

THR

MET

GLU

GLN

ALA

MET

ARG

LEU

41

LEU

ALA

PRO

ARG

VAL

GLN

PRO

GLY

ASP

MET

42

VAL

LEU

SER

PRO

ALA

CYS

ALA

SER

LEU

43

ASP

GLN

PHE

LYS

ASN

PHE

GLU

GLN

ARG

GLY

44

ASN

GLU

PHE

ALA

ARG

LEU

ALA

LYS

GLU

LEU

45

GLY

Samples:

sample_1: MurD, [U-100% 13C; U-100% 15N; U-100% 2H], 0.5 mM; H2O 90%; D2O 10%; Tris-HCl 20 mM; NaCl 200 mM; DTT 10 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 7.2; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY-HSQC	sample_1	isotropic	sample_conditions_1
TROSY-HN(CO)CA	sample_1	isotropic	sample_conditions_1
TROSY-HNCA	sample_1	isotropic	sample_conditions_1
TROSY-HNCA	sample_1	isotropic	sample_conditions_1
TROSY-HNCO	sample_1	isotropic	sample_conditions_1
TROSY-HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
TROSY-HNCACB	sample_1	isotropic	sample_conditions_1

Software:

OLIVIA, Masashi Yokochi - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Varian Unity Inova 800 MHz

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