BMRB Entry 16064

Name: Solution NMR structure of Bacteroides fragilis protein BF1650. Northeast Structural Genomics Consortium target BfR218
Published: 2009-05-07

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PDB ID: 2kc7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16064
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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 NMR structure of Bacteroides fragilis protein BF1650. Northeast Structural Genomics Consortium target BfR218

Deposition date:

2008-12-17

Original release date:

2009-05-07

Authors:

Eletsky, Alexander; Wu, Yibing; Sukumaran, Dinesh; Lee, Hsiau-Wei; Lee, Dong; Jiang, Mei; Foote, Erica; Xiao, Rong; Nair, Rajesh; Everett, John; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Prestegard, James; Szyperski, Thomas

Citation:

Citation: Eletsky, Alexander; Wu, Yibing; Sukumaran, Dinesh; Lee, Hsiau-Wei; Lee, Dong; Jiang, Mei; Foote, Erica; Xiao, Rong; Nair, Rajesh; Everett, John; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Prestegard, James; Szyperski, Thomas. "Solution NMR structure of Bacteroides fragilis protein BF1650. Northeast Structural Genomics Consortium target BfR218" Proteins: Struct. Funct. Genet. ., .-..

Assembly members:

Assembly members:
bfr218_protein, polymer, 99 residues, 11658.180 Da.

Natural source:

Natural source: Common Name: Bacteroides fragilis Taxonomy ID: 817 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacteroides fragilis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET 21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
bfr218_protein: MDQLKTIKELINQGDIENAL QALEEFLQTEPVGKDEAYYL MGNAYRKLGDWQKALNNYQS AIELNPDSPALQARKMVMDI LNFYNKDMYNQLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	408
15N chemical shifts	108
1H chemical shifts	692

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	bfr218_protein	1

Entities:

Entity 1, bfr218_protein 99 residues - 11658.180 Da.

The last 8 residues represent a non-native affinity tag

1

MET

ASP

GLN

LEU

LYS

THR

ILE

LYS

GLU

LEU

2

ILE

ASN

GLN

GLY

ASP

ILE

GLU

ASN

ALA

LEU

3

GLN

ALA

LEU

GLU

PHE

LEU

GLN

THR

GLU

4

PRO

VAL

GLY

LYS

ASP

GLU

ALA

TYR

LEU

5

MET

GLY

ASN

ALA

TYR

ARG

LYS

LEU

GLY

ASP

6

TRP

GLN

LYS

ALA

LEU

ASN

TYR

GLN

SER

7

ALA

ILE

GLU

LEU

ASN

PRO

ASP

SER

PRO

ALA

8

LEU

GLN

ALA

ARG

LYS

MET

VAL

MET

ASP

ILE

9

LEU

ASN

PHE

TYR

ASN

LYS

ASP

MET

TYR

ASN

10

GLN

LEU

GLU

HIS

Samples:

NC: MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; bfr218 protein, [U-100% 13C; U-100% 15N], 0.89 mM; H2O 90%; D2O 10%

NC5: MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; bfr218 protein, [U-5% 13C; U-100% 15N], 1 mM; H2O 90%; D2O 10%

NC5_phage: MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; bfr218 protein, [U-5% 13C; U-100% 15N], 1 mM; Pf1 phage 2.65 g/l; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 215 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC ali	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC aro	NC	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC ali	NC	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC aro	NC	isotropic	sample_conditions_1
3D HNNCO	NC	isotropic	sample_conditions_1
(4,3)D GFT CABCA(CO)NHN	NC	isotropic	sample_conditions_1
(4,3)D GFT HNNCABCA	NC	isotropic	sample_conditions_1
(4,3)D HABCAB(CO)NHN	NC	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY ali	NC	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY aro	NC	isotropic	sample_conditions_1
3D (H)CCH-TOCSY ali	NC	isotropic	sample_conditions_1
3D HN(CA)CO	NC	isotropic	sample_conditions_1
3D 1H-15N,13C NOESY	NC	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC ali 28ms	NC5	isotropic	sample_conditions_1
2D MEXICO	NC	isotropic	sample_conditions_1
2D 1H-15N HSQC	NC5_phage	anisotropic	sample_conditions_1
2D 1H-15N TROSY	NC5_phage	anisotropic	sample_conditions_1
2D 1H-15N HSQC	NC5	isotropic	sample_conditions_1
2D 1H-15N TROSY	NC5	isotropic	sample_conditions_1

Software:

VNMRJ v2.1B, Varian - collection

PROSA v6.0.2, Guntert - processing

CARA v1.8.4.2, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

TALOS v2007.068.09.07, Cornilescu, Delaglio and Bax - data analysis

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - structure solution

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.2.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

PSVS v1.3, Bhattacharya and Montelione - structure validation

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 600 MHz
Varian INOVA 600 MHz
Varian INOVA 500 MHz

PDB	2KC7
DBJ	BAD48398
EMBL	CAH07358 CBW22188 CDD38126 CUA18170
GB	AKA51470 EES87140 EEZ26991 EGN08814 EIK39617
REF	WP_005786499 WP_005800636 WP_032574002 WP_032576056 WP_042986797