BMRB Entry 30092

Name: NMR structure of pseudo receiver domain of CikA from Thermosynechococcus elongatus
Published: 2017-03-23

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PDB ID: 5jyu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30092
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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:

NMR structure of pseudo receiver domain of CikA from Thermosynechococcus elongatus

Deposition date:

2016-05-15

Original release date:

2017-03-23

Authors:

Tseng, Roger; Wang, Andy

Citation:

Citation: Tseng, Roger; Goularte, Nicolette; Chavan, Archana; Luu, Jansen; Cohen, Susan; Chang, Yong-Gang; Heisler, Joel; Li, Sheng; Michael, Alicia; Tripathi, Sarvind; Golden, Susan; LiWang, Andy; Partch, Carrie. "Structural basis of the day-night transition in a bacterial circadian clock" Science 355, 1174-1180 (2017).
PubMed: 28302851

Assembly members:

Assembly members:
Two-component sensor histidine kinase, polymer, 117 residues, 12899.736 Da.

Natural source:

Natural source: Common Name: cyanobacteria Taxonomy ID: 197221 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermosynechococcus elongatus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' Vector: pET28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Two-component sensor histidine kinase: EGRIVLVSEDEATSTLICSI LTTAGYQVIWLVDGEVERLL ALTPIAVLLAEPFSYGDVQE LVDQLRQRCTPEQLKIFILG SKGNYQGVDRYIPLPIHPES FLQQVTMGLTSLATSAQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	488
15N chemical shifts	110
1H chemical shifts	799

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 117 residues - 12899.736 Da.

1

GLU

GLY

ARG

ILE

VAL

LEU

VAL

SER

GLU

ASP

2

GLU

ALA

THR

SER

THR

LEU

ILE

CYS

SER

ILE

3

LEU

THR

ALA

GLY

TYR

GLN

VAL

ILE

TRP

4

LEU

VAL

ASP

GLY

GLU

VAL

GLU

ARG

LEU

5

ALA

LEU

THR

PRO

ILE

ALA

VAL

LEU

ALA

6

GLU

PRO

PHE

SER

TYR

GLY

ASP

VAL

GLN

GLU

7

LEU

VAL

ASP

GLN

LEU

ARG

GLN

ARG

CYS

THR

8

PRO

GLU

GLN

LEU

LYS

ILE

PHE

ILE

LEU

GLY

9

SER

LYS

GLY

ASN

TYR

GLN

GLY

VAL

ASP

ARG

10

TYR

ILE

PRO

LEU

PRO

ILE

HIS

PRO

GLU

SER

11

PHE

LEU

GLN

VAL

THR

MET

GLY

LEU

THR

12

SER

LEU

ALA

THR

SER

ALA

GLN

Samples:

sample_1: pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 1500 uM; H2O 95%; D2O 5%

sample_2: pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 1500 uM; H2O 0.04%; D2O 99.96%

sample_3: pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 300 uM; H2O 90%; D2O 10%

sample_4: pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 450 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D IPAP-HNCO	sample_4	anisotropic	sample_conditions_1
3D IPAP-HNCO	sample_3	isotropic	sample_conditions_1
3D IPAP-HNCO(CA)	sample_4	anisotropic	sample_conditions_1
3D IPAP-HNCO(CA)	sample_3	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

MARS, robust automatic backbone assignment of proteins Journal of Biomolecular NMR, 2004, Volume 30, Number 1, Page 11 Young-Sang Jung, Markus Zweckstetter - chemical shift assignment

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

X-PLOR NIH v2.39, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

XIPP, Garrett DS, Powers R, Gronenborn AM, Clore GM. J Magn Reson. 2011 Dec;213(2):357-63. doi: 10.1016/j.jmr.2011.09.007. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams http://spin.niddk.nih.gov/dgarrett/Xipp/xipp.html - peak picking

NMR spectrometers:

Bruker AvanceIII 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks