BMRB Entry 15717

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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/BMR15717
MolProbity Validation Chart

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Title:
SOLUTION STRUCTURE OF A CYANOBACTERIAL PHYTOCHROME GAF DOMAIN IN THE RED LIGHT-ABSORBING GROUND STATE
Deposition date:
2008-04-04
Original release date:
2008-09-12
Authors:
Cornilescu, Claudia; Cornilescu, Gabriel; Ulijasz, Andrew; Vierstra, Richard; Markley, John
Citation:

Citation: Cornilescu, Gabriel; Ulijasz, Andrew; Cornilescu, Claudia; Markley, John; Vierstra, Richard. "SOLUTION STRUCTURE OF A CYANOBACTERIAL PHYTOCHROME GAF DOMAIN IN THE RED LIGHT-ABSORBING GROUND STATE"  J. Mol. Biol. 383, 403-413 (2008).
PubMed: 18762196

Assembly members:

Assembly members:
SyB-Cph1(GAF), polymer, 208 residues, 19825.713 Da.

Natural source:

Natural source:   Common Name: Thermosynechococcus elongatus BP-1   Taxonomy ID: 197221   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Synechococcus OS-B'

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-4T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SyB-Cph1(GAF): MDTETWAAAARPSRDALINR ITHQIRQSLELDQILRATVE EVRAFLGTDRVKVYRFDPEG HGTVVAEARGGERLPSLLGL TFPAGDIPEEARRLFRLAQV RVIVDVEAQSRSISQPESWG LSARVPLGEPLQRPVDPXHV HYLKSMGVASSLVVPLMHHQ ELWGLLVSHHAEPRPYSQEE LQVVQLLADQVSIAIAQAEL SLHHHHHH

Data sets:
Data typeCount
13C chemical shifts587
15N chemical shifts148
1H chemical shifts755
residual dipolar couplings250

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1SyB-Cph1(GAF)1

Entities:

Entity 1, SyB-Cph1(GAF) 208 residues - 19825.713 Da.

1   METASPTHRGLUTHRTRPALAALAALAALA
2   ARGPROSERARGASPALALEUILEASNARG
3   ILETHRHISGLNILEARGGLNSERLEUGLU
4   LEUASPGLNILELEUARGALATHRVALGLU
5   GLUVALARGALAPHELEUGLYTHRASPARG
6   VALLYSVALTYRARGPHEASPPROGLUGLY
7   HISGLYTHRVALVALALAGLUALAARGGLY
8   GLYGLUARGLEUPROSERLEULEUGLYLEU
9   THRPHEPROALAGLYASPILEPROGLUGLU
10   ALAARGARGLEUPHEARGLEUALAGLNVAL
11   ARGVALILEVALASPVALGLUALAGLNSER
12   ARGSERILESERGLNPROGLUSERTRPGLY
13   LEUSERALAARGVALPROLEUGLYGLUPRO
14   LEUGLNARGPROVALASPPROCYCHISVAL
15   HISTYRLEULYSSERMETGLYVALALASER
16   SERLEUVALVALPROLEUMETHISHISGLN
17   GLULEUTRPGLYLEULEUVALSERHISHIS
18   ALAGLUPROARGPROTYRSERGLNGLUGLU
19   LEUGLNVALVALGLNLEULEUALAASPGLN
20   VALSERILEALAILEALAGLNALAGLULEU
21   SERLEUHISHISHISHISHISHIS

Samples:

sample_1: SyB-Cph1(GAF), [U-13C; U-15N], 1.7 mM; PHYCOCYANOBILIN 1.7 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_2: SyB-Cph1(GAF) 2 mM; PHYCOCYANOBILIN, [U-15N], 2 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_3: SyB-Cph1(GAF) 1 mM; PHYCOCYANOBILIN, [U-13C], 1 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_4: SyB-Cph1(GAF), [U-13C; U-15N], 1 mM; PHYCOCYANOBILIN 1 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_5: SyB-Cph1(GAF), [U-13C; U-15N], 1 mM; PHYCOCYANOBILIN 1 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_6: SyB-Cph1(GAF) 0.5 mM; PHYCOCYANOBILIN, [U-13C], 0.5 mM; Tris-DCl, [U-2H], 10 mM; NaN3 0.03%

sample_conditions_1: ionic strength: 0.01 M; pH: 8.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.01 M; pH: 8.5; pressure: 1 atm; temperature: 306 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCO antiphasesample_5anisotropicsample_conditions_2
3D HCA(CO)N antiphasesample_5anisotropicsample_conditions_2
J modulated 2D 1H-13C HSQCsample_6anisotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

VNMRJ, Varian - collection

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, data analysis, peak picking

PIPP, Garrett - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB

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