BMRB Entry 18411

Name: Solution structure of a putative protein disulfide isomerase from Bacteroides thetaiotaomicron
Published: 2012-05-22

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PDB ID: 2ls5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18411
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of a putative protein disulfide isomerase from Bacteroides thetaiotaomicron

Deposition date:

2012-04-20

Original release date:

2012-05-22

Authors:

Harris, R.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.

Citation:

Citation: Harris, R.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.. "Solution structure of a putative protein disulfide isomerase from Bacteroides thetaiotaomicron" To be published ., .-..

Assembly members:

Assembly members:
putative_protein_disulfide_isomerase, polymer, 159 residues, 18022.982 Da.

Natural source:

Natural source: Common Name: Bacteroides fragilis subsp. thetaiotaomicron Taxonomy ID: 818 Superkingdom: Baceteria Kingdom: not available Genus/species: Bacteroides thetaiotaomicron

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: modified pET26

Entity Sequences (FASTA):

Entity Sequences (FASTA):
putative_protein_disulfide_isomerase: MSLGYIVRIGEMAPDFTITL TDGKQVTLSSLRGKVVMLQF TASWCGVCRKEMPFIEKDIW LKHKDNADFALIGIDRDEPL EKVLAFAKSTGVTYPLGLDP GADIFAKYALRDAGITRNVL IDREGKIVKLTRLYNEEEFA SLVQQINEMLKEGHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	695
15N chemical shifts	147
1H chemical shifts	1112

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	putative protein disulfide isomerase	1

Entities:

Entity 1, putative protein disulfide isomerase 159 residues - 18022.982 Da.

expressed sequence start-stop 53-200 N-term cloning artifact: MSL C-term cloning artifact: EGHHHHHH

1

MET

SER

LEU

GLY

TYR

ILE

VAL

ARG

ILE

GLY

2

GLU

MET

ALA

PRO

ASP

PHE

THR

ILE

THR

LEU

3

THR

ASP

GLY

LYS

GLN

VAL

THR

LEU

SER

4

LEU

ARG

GLY

LYS

VAL

MET

LEU

GLN

PHE

5

THR

ALA

SER

TRP

CYS

GLY

VAL

CYS

ARG

LYS

6

GLU

MET

PRO

PHE

ILE

GLU

LYS

ASP

ILE

TRP

7

LEU

LYS

HIS

LYS

ASP

ASN

ALA

ASP

PHE

ALA

8

LEU

ILE

GLY

ILE

ASP

ARG

ASP

GLU

PRO

LEU

9

GLU

LYS

VAL

LEU

ALA

PHE

ALA

LYS

SER

THR

10

GLY

VAL

THR

TYR

PRO

LEU

GLY

LEU

ASP

PRO

11

GLY

ALA

ASP

ILE

PHE

ALA

LYS

TYR

ALA

LEU

12

ARG

ASP

ALA

GLY

ILE

THR

ARG

ASN

VAL

LEU

13

ILE

ASP

ARG

GLU

GLY

LYS

ILE

VAL

LYS

LEU

14

THR

ARG

LEU

TYR

ASN

GLU

PHE

ALA

15

SER

LEU

VAL

GLN

ILE

ASN

GLU

MET

LEU

16

LYS

GLU

GLY

HIS

Samples:

sample_1: putative protein disulfide isomerase, [U-13C; U-15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 1 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_2: putative protein disulfide isomerase, [U-13C; U-15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 1 mM; EDTA 1 mM; D2O 100%

sample_conditions_1: ionic strength: 70 mM; pH: 7.4; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC	sample_1	isotropic	sample_conditions_1
15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C CT-HSQC	sample_2	isotropic	sample_conditions_1
aromatic 13C CT-HSQC	sample_2	isotropic	sample_conditions_1
13C NOESY-HSQC	sample_2	isotropic	sample_conditions_1
13C aromatic NOESY-HSQC	sample_2	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
HNCACO	sample_1	isotropic	sample_conditions_1
HNCA	sample_1	isotropic	sample_conditions_1
HNCOCA	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA v2.3, Linge, O'Donoghue and Nilges - data analysis

NMRPipe v5.4, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMRJ v2.2D, Varian - collection

TOPSPIN v2.1, Bruker Biospin - collection

CCPN v2.1.5, CCPN - chemical shift assignment, data analysis, peak picking

MDDNMR v2.0, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI v1.0, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

NMR spectrometers:

Varian Inova 600 MHz
Bruker Avance 700 MHz
Bruker Avance 900 MHz

PDB	2LS5
EMBL	CDE75657 CUN16544 CUP25757 CUQ38286
GB	AAO76690 ALJ41047 EES65847 EFI03545 EOS03325
REF	NP_810496 WP_011107875 WP_032813276 WP_055221217 WP_055229342