BMRB Entry 16135

Name: Sequence-specific 1H, 15N, and 13C resonance assignments of the 23.7 kDa homodimeric toxin CcdB from Vibrio fischeri.
Published: 2009-04-14

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PDB ID: 2kmt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16135
MolProbity Validation Chart

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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:

Sequence-specific 1H, 15N, and 13C resonance assignments of the 23.7 kDa homodimeric toxin CcdB from Vibrio fischeri.

Deposition date:

2009-01-23

Original release date:

2009-04-14

Authors:

Respondek, Michal; Buts, Lieven; Loris, Remy; Zangger, Klaus

Citation:

Citation: Respondek, Michal; Buts, Lieven; De Jonge, Natalie; Haesaerts, Sarah; Loris, Remy; Van Melderen, Laurence; Wyns, Lode; Zangger, Klaus. "Sequence-specific 1H, 15N and 13C resonance assignments of the 23.7-kDa homodimeric toxin CcdB from Vibrio fischeri" Biomol. NMR Assignments 3, 145-147 (2009).
PubMed: 19636967

Assembly members:

Assembly members:
CcdB, polymer, 105 residues, 11.87 Da.

Natural source:

Natural source: Common Name: Vibrio fischeri Taxonomy ID: 668 Superkingdom: Bacteria Kingdom: not available Genus/species: Vibrio fischeri

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pKK223-3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CcdB: MSQFTLYKNKDKSSAKTYPY FVDVQSDLLDNLNTRLVIPL TPIELLDKKAPSHLCPTIHI DEGDFIMLTQQMTSVPVKIL SEPVNELSTFRNEIIAAIDF LITGI

Data sets:

assigned_chemical_shifts
- assignments_ccdB

Data type	Count
13C chemical shifts	450
15N chemical shifts	98
1H chemical shifts	629

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CcdB, chain 1	1
2	CcdB, chain 2	1

Entities:

Entity 1, CcdB, chain 1 105 residues - 11.87 Da.

1

MET

SER

GLN

PHE

THR

LEU

TYR

LYS

ASN

LYS

2

ASP

LYS

SER

ALA

LYS

THR

TYR

PRO

TYR

3

PHE

VAL

ASP

VAL

GLN

SER

ASP

LEU

ASP

4

ASN

LEU

ASN

THR

ARG

LEU

VAL

ILE

PRO

LEU

5

THR

PRO

ILE

GLU

LEU

ASP

LYS

ALA

6

PRO

SER

HIS

LEU

CYS

PRO

THR

ILE

HIS

ILE

7

ASP

GLU

GLY

ASP

PHE

ILE

MET

LEU

THR

GLN

8

GLN

MET

THR

SER

VAL

PRO

VAL

LYS

ILE

LEU

9

SER

GLU

PRO

VAL

ASN

GLU

LEU

SER

THR

PHE

10

ARG

ASN

GLU

ILE

ALA

ILE

ASP

PHE

11

LEU

ILE

THR

GLY

ILE

Samples:

sample_1: CcdB, [U-100% 13C; U-100% 15N], 4-6 mg; sodium phosphate 50 mM; sodium azide 0.02%; D2O 10%; H2O 90%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

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

NMRView v5.2.2, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Bruker Avance 500 MHz

PDB	2KMT 3JRZ 3JSC 3TCJ 4ELY 4ELZ
GB	AAO38253 ACH63869 EHN67942
REF	WP_005424093 WP_012535038 WP_054776277