BMRB Entry 30093

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30093
MolProbity Validation Chart

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Title:
NMR structure of foldswitch-stablized KaiB in complex with 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.
Circadian clock protein KaiB, polymer, 106 residues, 11779.870 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'

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Two-component sensor histidine kinase: EGRIVLVSEDEATSTLICSI LTTAGYQVIWLVDGEVERLL ALTPIAVLLAEPFSYGDVQE LVDQLRQRCTPEQLKIFILG SKGNYQGVDRYIPLPIHPES FLQQVTMGLTSLATSAQ
Circadian clock protein KaiB: MAPLRKTAVLKLYVAGNTPN SVRALKTLANILEKEFKGVY ALKVIDVLKNPQLAEEDKIL ATPTLAKVLPPPVRRIIGDL SNREKVLIALRLLAEEIGDY KDDDDK

Data typeCount
13C chemical shifts932
15N chemical shifts200
1H chemical shifts1505

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 117 residues - 12899.736 Da.

1   GLUGLYARGILEVALLEUVALSERGLUASP
2   GLUALATHRSERTHRLEUILECYSSERILE
3   LEUTHRTHRALAGLYTYRGLNVALILETRP
4   LEUVALASPGLYGLUVALGLUARGLEULEU
5   ALALEUTHRPROILEALAVALLEULEUALA
6   GLUPROPHESERTYRGLYASPVALGLNGLU
7   LEUVALASPGLNLEUARGGLNARGCYSTHR
8   PROGLUGLNLEULYSILEPHEILELEUGLY
9   SERLYSGLYASNTYRGLNGLYVALASPARG
10   TYRILEPROLEUPROILEHISPROGLUSER
11   PHELEUGLNGLNVALTHRMETGLYLEUTHR
12   SERLEUALATHRSERALAGLN

Entity 2, entity_2 106 residues - 11779.870 Da.

1   METALAPROLEUARGLYSTHRALAVALLEU
2   LYSLEUTYRVALALAGLYASNTHRPROASN
3   SERVALARGALALEULYSTHRLEUALAASN
4   ILELEUGLULYSGLUPHELYSGLYVALTYR
5   ALALEULYSVALILEASPVALLEULYSASN
6   PROGLNLEUALAGLUGLUASPLYSILELEU
7   ALATHRPROTHRLEUALALYSVALLEUPRO
8   PROPROVALARGARGILEILEGLYASPLEU
9   SERASNARGGLULYSVALLEUILEALALEU
10   ARGLEULEUALAGLUGLUILEGLYASPTYR
11   LYSASPASPASPASPLYS

Samples:

sample_1: KaiB mutant-N29A 880 uM; pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 800 uM; H2O 95%; D2O 5%

sample_10: KaiB mutant-N29A 440 uM; pseudo receiver domain of CikA, [U-99% 15N], 400 uM; H2O 90%; D2O 10%

sample_11: KaiB mutant-N29A, [U-99% 13C; U-99% 15N], 400 uM; pseudo receiver domain of CikA 440 uM; H2O 90%; D2O 10%

sample_12: KaiB mutant-N29A, [U-99% 13C; U-99% 15N], 700 uM; pseudo receiver domain of CikA 770 uM; H2O 90%; D2O 10%

sample_13: KaiB mutant-N29A, [U-99% 15N], 400 uM; pseudo receiver domain of CikA 440 uM; H2O 90%; D2O 10%

sample_14: KaiB mutant-N29A, [U-99% 15N], 400 uM; pseudo receiver domain of CikA 440 uM; H2O 90%; D2O 10%

sample_15: KaiB mutant-N29A 880 uM; pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 800 uM; D2O 100%

sample_16: KaiB mutant-N29A, [U-99% 13C; U-99% 15N], 800 uM; pseudo receiver domain of CikA 880 uM; D2O 100%

sample_2: KaiB mutant-N29A 880 uM; pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 800 uM; D2O 100%

sample_3: KaiB mutant-N29A, [U-99% 13C; U-99% 15N], 800 uM; pseudo receiver domain of CikA 880 uM; H2O 95%; D2O 5%

sample_4: KaiB mutant-N29A, [U-99% 13C; U-99% 15N], 800 uM; pseudo receiver domain of CikA 880 uM; D2O 100%

sample_5: KaiB mutant-N29A, [U-100% 13C], 880 uM; pseudo receiver domain of CikA, [U-100% 15N], 800 uM; H2O 95%; D2O 5%

sample_6: KaiB mutant-N29A, [U-100% 15N], 800 uM; pseudo receiver domain of CikA, [U-100% 13C], 880 uM; H2O 95%; D2O 5%

sample_7: KaiB mutant-N29A 440 uM; pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 400 uM; H2O 90%; D2O 10%

sample_8: KaiB mutant-N29A 715 uM; pseudo receiver domain of CikA, [U-99% 13C; U-99% 15N], 650 uM; H2O 90%; D2O 10%

sample_9: KaiB mutant-N29A 440 uM; pseudo receiver domain of CikA, [U-99% 15N], 400 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 mM; pH: 7; pressure: 1 atm; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
15N, 13C edited 4D NOESY-HSQCsample_5isotropicsample_conditions_1
2D IPAP-1H-15N HSQCsample_10anisotropicsample_conditions_1
2D IPAP-1H-15N HSQCsample_9isotropicsample_conditions_1
3D IPAP-HNCOsample_8anisotropicsample_conditions_1
3D IPAP-HNCOsample_7isotropicsample_conditions_1
3D IPAP-HNCO(CA)sample_8anisotropicsample_conditions_1
3D IPAP-HNCO(CA)sample_7isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D 13C edited 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 15N edited 1H-15N NOESYsample_1isotropicsample_conditions_1
13C-edited, 12C-filtered 3D NOESY-HSQCsample_16isotropicsample_conditions_1
15N, 13C edited 4D NOESY-HSQCsample_6isotropicsample_conditions_1
2D IPAP-1H-15N HSQCsample_14anisotropicsample_conditions_1
2D IPAP-1H-15N HSQCsample_13isotropicsample_conditions_1
3D IPAP-HNCOsample_12anisotropicsample_conditions_1
3D IPAP-HNCOsample_11isotropicsample_conditions_1
3D IPAP-HNCO(CA)sample_12anisotropicsample_conditions_1
3D IPAP-HNCO(CA)sample_11isotropicsample_conditions_1
3D HCA(CO)Nsample_4isotropicsample_conditions_1
3D HCANsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D HCCH-COSYsample_4isotropicsample_conditions_1
3D 13C edited 1H-13C NOESYsample_4isotropicsample_conditions_1
3D 15N edited 1H-15N NOESYsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CO)CACBsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
13C-edited, 12C-filtered 3D NOESY-HSQCsample_15isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_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

PIPP, Garrett - peak picking

X-PLOR NIH, 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