BMRB Entry 16729

Name: NMR assignment of Salmonella typhimurium tip protein SipD
Published: 2010-05-03

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16729

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR assignment of Salmonella typhimurium tip protein SipD

Deposition date:

2010-02-16

Original release date:

2010-05-03

Authors:

Wang, Yu; Nordhues, Bryce; Zhong, Dalian; De Guzman, Roberto

Citation:

Citation: Wang, Yu; Nordhues, Bryce; Zhong, Dalian; De Guzman, Roberto. "NMR characterization of the interaction of the Salmonella type III secretion system protein SipD and bile salts." Biochemistry 49, 4220-4226 (2010).
PubMed: 20397637

Assembly members:

Assembly members:
SipD, polymer, 343 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Salmonella typhimurium Taxonomy ID: 90371 Superkingdom: Bacteria Kingdom: not available Genus/species: Salmonella typhimurium

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SipD: MLNIQNYSASPHPGIVAERP QTPSASEHVETAVVPSTTEH RGTDIISLSQAATKIHQAQQ TLQSTPPISEENNDERTLAR QQLTSSLNALAKSGVSLSAE QNENLRSAFSAPTSALFSAS PMAQPRTTISDAEIWDMVSQ NISAIGDSYLGVYENVVAVY TDFYQAFSDILSKMGGWLLP GKDGNTVKLDVTSLKNDLNS LVNKYNQINSNTVLFPAQSG SGVKVATEAEARQWLSELNL PNSCLKSYGSGYVVTVDLTP LQKMVQDIDGLGAPGKDSKL EMDNAKYQAWQSGFKAQEEN MKTTLQTLTQKYSNANSLYD NLVKVLSSTISSSLETAKSF LQG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	801
15N chemical shifts	274
1H chemical shifts	265

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SipDND38	1

Entities:

Entity 1, SipDND38 343 residues - Formula weight is not available

1

MET

LEU

ASN

ILE

GLN

ASN

TYR

SER

ALA

SER

2

PRO

HIS

PRO

GLY

ILE

VAL

ALA

GLU

ARG

PRO

3

GLN

THR

PRO

SER

ALA

SER

GLU

HIS

VAL

GLU

4

THR

ALA

VAL

PRO

SER

THR

GLU

HIS

5

ARG

GLY

THR

ASP

ILE

SER

LEU

SER

GLN

6

ALA

THR

LYS

ILE

HIS

GLN

ALA

GLN

7

THR

LEU

GLN

SER

THR

PRO

ILE

SER

GLU

8

GLU

ASN

ASP

GLU

ARG

THR

LEU

ALA

ARG

9

GLN

LEU

THR

SER

LEU

ASN

ALA

LEU

10

ALA

LYS

SER

GLY

VAL

SER

LEU

SER

ALA

GLU

11

GLN

ASN

GLU

ASN

LEU

ARG

SER

ALA

PHE

SER

12

ALA

PRO

THR

SER

ALA

LEU

PHE

SER

ALA

SER

13

PRO

MET

ALA

GLN

PRO

ARG

THR

ILE

SER

14

ASP

ALA

GLU

ILE

TRP

ASP

MET

VAL

SER

GLN

15

ASN

ILE

SER

ALA

ILE

GLY

ASP

SER

TYR

LEU

16

GLY

VAL

TYR

GLU

ASN

VAL

ALA

VAL

TYR

17

THR

ASP

PHE

TYR

GLN

ALA

PHE

SER

ASP

ILE

18

LEU

SER

LYS

MET

GLY

TRP

LEU

PRO

19

GLY

LYS

ASP

GLY

ASN

THR

VAL

LYS

LEU

ASP

20

VAL

THR

SER

LEU

LYS

ASN

ASP

LEU

ASN

SER

21

LEU

VAL

ASN

LYS

TYR

ASN

GLN

ILE

ASN

SER

22

ASN

THR

VAL

LEU

PHE

PRO

ALA

GLN

SER

GLY

23

SER

GLY

VAL

LYS

VAL

ALA

THR

GLU

ALA

GLU

24

ALA

ARG

GLN

TRP

LEU

SER

GLU

LEU

ASN

LEU

25

PRO

ASN

SER

CYS

LEU

LYS

SER

TYR

GLY

SER

26

GLY

TYR

VAL

THR

VAL

ASP

LEU

THR

PRO

27

LEU

GLN

LYS

MET

VAL

GLN

ASP

ILE

ASP

GLY

28

LEU

GLY

ALA

PRO

GLY

LYS

ASP

SER

LYS

LEU

29

GLU

MET

ASP

ASN

ALA

LYS

TYR

GLN

ALA

TRP

30

GLN

SER

GLY

PHE

LYS

ALA

GLN

GLU

ASN

31

MET

LYS

THR

LEU

GLN

THR

LEU

THR

GLN

32

LYS

TYR

SER

ASN

ALA

ASN

SER

LEU

TYR

ASP

33

ASN

LEU

VAL

LYS

VAL

LEU

SER

THR

ILE

34

SER

LEU

GLU

THR

ALA

LYS

SER

PHE

35

LEU

GLN

GLY

Samples:

sample_1: SipD, [U-98% 15N], 0.6 ± 0.05 mM; SipD, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 ± 0.05 mM; H2O 90%; D2O 10%; sodium phosphate 10 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 0.08 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

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

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2YM0 2YM9 3NZZ 3O00 3O01 3O02 3ZQB 3ZQE
DBJ	BAJ37875 BAP08788
EMBL	CAR34302 CAR38594 CBG25852 CBW18960 CBY97053
GB	AAA86617 AAC43548 AAL21763 AAX66721 ABX68926
REF	NP_461804 WP_000932241 WP_000932242 WP_000932245 WP_000932246
SP	Q56026
AlphaFold	Q56026