BMRB Entry 16030

Name: Solution structure of protein BPP2914 from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR206
Published: 2009-03-05

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PDB ID: 2kat
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16030
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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:

Solution structure of protein BPP2914 from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR206

Deposition date:

2008-11-14

Original release date:

2009-03-05

Authors:

Wu, Yibing; Mills, Jeffrey; Wang, Dongyan; Jiang, Mei; Foote, Erica; Xiao, Rong; Sathyamoorthy, Bharathwaj; Sukumaran, Dinesh; Nair, Rajesh; Everett, John; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas

Citation:

Citation: Wu, Yibing; Mills, Jeffrey; Wang, Dongyan; Jiang, Mei; Foote, Erica; Xiao, Rong; Sathyamoorthy, Bharathwaj; Sukumaran, Dinesh; Nair, Rajesh; Everett, John; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas. "Solution structure of protein BPP2914 from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR206" .

Assembly members:

Assembly members:
BPP, polymer, 115 residues, 13089.824 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Eubacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
BPP: MQAITERLEAMLAQGTDNML LRFTLGKTYAEHEQFDAALP HLRAALDFDPTYSVAWKWLG KTLQGQGDRAGARQAWESGL AAAQSRGDQQVVKELQVFLR RLAREDALEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	376
15N chemical shifts	125
1H chemical shifts	797

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	BPP	1

Entities:

Entity 1, BPP 115 residues - 13089.824 Da.

1

MET

GLN

ALA

ILE

THR

GLU

ARG

LEU

GLU

ALA

2

MET

LEU

ALA

GLN

GLY

THR

ASP

ASN

MET

LEU

3

LEU

ARG

PHE

THR

LEU

GLY

LYS

THR

TYR

ALA

4

GLU

HIS

GLU

GLN

PHE

ASP

ALA

LEU

PRO

5

HIS

LEU

ARG

ALA

LEU

ASP

PHE

ASP

PRO

6

THR

TYR

SER

VAL

ALA

TRP

LYS

TRP

LEU

GLY

7

LYS

THR

LEU

GLN

GLY

GLN

GLY

ASP

ARG

ALA

8

GLY

ALA

ARG

GLN

ALA

TRP

GLU

SER

GLY

LEU

9

ALA

GLN

SER

ARG

GLY

ASP

GLN

10

VAL

LYS

GLU

LEU

GLN

VAL

PHE

LEU

ARG

11

ARG

LEU

ALA

ARG

GLU

ASP

ALA

LEU

GLU

HIS

12

HIS

Samples:

sample_2: BPP, [U-5% 13C; U-100% 15N], 0.3 mM; H2O 90%; D2O 10%; Ammonium Acetate 20 mM; NaCl 200 mM; CaCl2 5 mM; DTT 10 mM; DSS 50 uM; NaN3 .02%

sample_1: BPP, [U-100% 13C; U-100% 15N], 0.3 mM; H2O 90%; D2O 10%; Ammonium Acetate 20 mM; NaCl 200 mM; CaCl2 5 mM; DTT 10 mM; DSS 50 uM; NaN3 .02%

sample_conditions_1: ionic strength: 0.2 M; pH: 4.5; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D, 15N-13C RESOLVED SIMULTANIOUS NOESY	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

XEASY, Bartels et al. - peak picking

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

PSVS, Bhattacharya and Montelione - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz

PDB	2KAT
DBJ	BAO69438
EMBL	CAE33376 CAE38207 CAE41600 CCJ49952 CCJ52604
GB	AEE66689 AIW92849 AIW95226 AJB27345 ALH49899
REF	NP_880070 WP_003811313 WP_015039931 WP_029443804 WP_041937430