BMRB Entry 17496

Title:
Solution Structure of the PilZ Domain Protein PA4608 Complex with Cyclic Di-GMP Identifies Charge Clustering as Molecular Readout
Deposition date:
2011-02-28
Original release date:
2011-06-01
Authors:
Habazettl, Judith; Allan, Martin; Jenal, Urs; Grzesiek, Stephan
Citation:

Citation: Habazettl, Judith; Allan, Martin; Jenal, Urs; Grzesiek, Stephan. "Solution Structure of the PilZ Domain Protein PA4608 Complex with Cyclic di-GMP Identifies Charge Clustering as Molecular Readout."  J. Biol. Chem. 286, 14304-14314 (2011).
PubMed: 21310957

Assembly members:

Assembly members:
PA4608, polymer, 145 residues, 14593.500 Da.
C2E, non-polymer, 690.411 Da.

Natural source:

Natural source:   Common Name: Pseudomonas aeruginosa   Taxonomy ID: 287   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Pseudomonas aeruginosa

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET15

Data sets:
Data typeCount
13C chemical shifts573
15N chemical shifts153
1H chemical shifts918

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PA46081
2C2E_12
3C2E_22

Entities:

Entity 1, PA4608 145 residues - 14593.500 Da.

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METSERASPGLNHISASPGLUARGARGARG
4   PHEHISARGILEALAPHEASPALAASPSER
5   GLUILELEUGLNGLYGLUARGARGTRPGLU
6   VALLEULEUHISASPVALSERLEUHISGLY
7   ILELEUVALGLYGLNPROGLNASPTRPASN
8   GLYASPPROGLNARGPROPHEGLUALAARG
9   LEUTYRLEUGLYLEUASPVALLEUILEARG
10   METGLUILESERLEUALATRPALAARGASP
11   GLYLEULEUGLYPHEGLUCYSGLNHISILE
12   ASPLEUASPSERILESERHISLEUARGARG
13   LEUVALGLULEUASNLEUGLYASPGLUGLU
14   LEULEUGLUARGGLULEUALALEULEUVAL
15   SERALAHISASPASP

Entity 2, C2E_1 - C20 H24 N10 O14 P2 - 690.411 Da.

1   C2E

Samples:

sample_1: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.8 mM; C2E 1.6 mM; H2O 95%; D2O 5%

sample_7: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.1 mM; H2O 95%; D2O 5%

sample_2: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.8 mM; C2E 1.6 mM; D2O 100%

sample_3: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.0 mM; C2E, [U-99% 13C; U-99% 15N], 2.0 mM; D2O 100%

sample_4: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.6 mM; C2E, [U-99% 13C; U-99% 15N], 1.2 mM; H2O 93%; D2O 7%

sample_5: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.0 mM; C2E, [U-99% 13C; U-99% 15N], 2.0 mM; H2O 95%; D2O 5%

sample_6: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.2 mM; C2E, [U-99% 13C; U-99% 15N], 0.6 mM; C2E 0.6 mM; H2O 95%; D2O 5%

sample_8: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 15N], 0.5 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.7; pressure: 1 atm; temperature: 293 K

sample_conditions_2: pH: 6.7; pressure: 1 atm; temperature: 313 K

sample_conditions_3: pH: 6.7; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSY (Ribose)sample_3isotropicsample_conditions_1
3D HCCH-COSY (Ribose)sample_3isotropicsample_conditions_3
HAHBsample_2isotropicsample_conditions_1
HAHB (Ribose)sample_3isotropicsample_conditions_1
HAHB (Ribose)sample_4anisotropicsample_conditions_1
13C-{13Cg}spin-echo difference H-15N HSQCsample_5isotropicsample_conditions_1
15N-{13Cg} spin-echo diference H-15N HAQCsample_5isotropicsample_conditions_1
Methyl Csample_2isotropicsample_conditions_1
Methyl Nsample_2isotropicsample_conditions_1
3D 1H-15N ROESYsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY(aliphatic)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY (aromatic)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY(Ribose)sample_5isotropicsample_conditions_1
4D 13C-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESY (filtered against H bound to 13C, 15N)sample_1isotropicsample_conditions_1
IPAP 1H-15N HSQCsample_1isotropicsample_conditions_1
IPAP 1H-15N HSQCsample_4anisotropicsample_conditions_1
J-resolved ct 13C-HSQCsample_5isotropicsample_conditions_1
J-resolved ct 13C-HSQCsample_4anisotropicsample_conditions_1
2D H-resolved 15N EXSYsample_6isotropicsample_conditions_1
3D H-15N-15N EXSYsample_6isotropicsample_conditions_2
IPAP 1H-15N HSQCsample_7isotropicsample_conditions_1
IPAP 1H-15N HSQCsample_8anisotropicsample_conditions_1
2D 1H resolved 15N EXSYsample_6isotropicsample_conditions_3
2D 1H-resolved 15N EXSYsample_6isotropicsample_conditions_2
2D 1H-15N HSQCsample_7isotropicsample_conditions_1
15N Relaxationsample_7isotropicsample_conditions_1
15N Relaxationsample_1isotropicsample_conditions_1

Software:

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

PIPP, Garrett - peak picking

SPARKY, Goddard - chemical shift assignment, structure solution

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

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker DPX 800 MHz

Related Database Links:

PDB
DBJ BAK87859 BAP21553 BAP53111 BAQ42358 BAR70033
EMBL CAW29747 CCQ83984 CDH73305 CDH79614 CDI93152
GB AAG07996 ABJ13986 ABR81943 AEO77182 AFM67158
REF NP_253298 WP_003094864 WP_003123411 WP_003153057 WP_024914602
SP Q9HVI1
AlphaFold Q9HVI1

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