BMRB Entry 27876

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27876

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Title:
NMR resonance assignment for the GSPII-C domain of PilF from Thermus thermophilus in complex with c-di-GMP
Deposition date:
2019-04-10
Original release date:
2019-08-14
Authors:
Keller, Heiko; Duchardt-Ferner, Elke; Woehnert, Jens
Citation:

Citation: Keller, Heiko; Kruse, Kerstin; Averhoff, Beate; Duchardt-Ferner, Elke; Woehnert, Jens. "NMR resonance assignments for the GSPII-C domain of the PilF ATPase from Thermus thermophilus in complex with c-di-GMP"  Biomol. NMR Assignments 13, 361-366 (2019).
PubMed: 31372934

Assembly members:

Assembly members:
PilF_294-482, polymer, 191 residues, 21223 Da.
entity_C2E, non-polymer, 690.411 Da.

Natural source:

Natural source:   Common Name: Thermus thermophilus   Taxonomy ID: 274   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Thermus thermophilus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Thermus thermophilus   Vector: pET-11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PilF_294-482: GSLFRRAYPQKNRLGEVLVQ EGKLSREALKEALEVQKGLP RAKPLGEILVELGLARPEDV EEALQKQRRGGGRLEDTLVQ SGKLRPEALAQAVATQLGYP YVDPEEDPPDPGAPLLLPED LCRRYGVFPHRLEGNRLVLL MKDPRNILALDDVRLALKRK GLNYEVAPAVATEAAITKLI ERFYGKAELSE

Data typeCount
13C chemical shifts858
15N chemical shifts178
1H chemical shifts1370

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1PilF 294-4821
2c-di-GMP2

Entities:

Entity 1, PilF 294-482 191 residues - 21223 Da.

Residues 1-2 represent a non-native tag remaining from TEV cleavage.

1   GLYSERLEUPHEARGARGALATYRPROGLN
2   LYSASNARGLEUGLYGLUVALLEUVALGLN
3   GLUGLYLYSLEUSERARGGLUALALEULYS
4   GLUALALEUGLUVALGLNLYSGLYLEUPRO
5   ARGALALYSPROLEUGLYGLUILELEUVAL
6   GLULEUGLYLEUALAARGPROGLUASPVAL
7   GLUGLUALALEUGLNLYSGLNARGARGGLY
8   GLYGLYARGLEUGLUASPTHRLEUVALGLN
9   SERGLYLYSLEUARGPROGLUALALEUALA
10   GLNALAVALALATHRGLNLEUGLYTYRPRO
11   TYRVALASPPROGLUGLUASPPROPROASP
12   PROGLYALAPROLEULEULEUPROGLUASP
13   LEUCYSARGARGTYRGLYVALPHEPROHIS
14   ARGLEUGLUGLYASNARGLEUVALLEULEU
15   METLYSASPPROARGASNILELEUALALEU
16   ASPASPVALARGLEUALALEULYSARGLYS
17   GLYLEUASNTYRGLUVALALAPROALAVAL
18   ALATHRGLUALAALAILETHRLYSLEUILE
19   GLUARGPHETYRGLYLYSALAGLULEUSER
20   GLU

Entity 2, c-di-GMP - C20 H24 N10 O14 P2 - 690.411 Da.

1   C2E

Samples:

13C15N: PilF 294-482, [U-13C; U-15N], 483 uM; c-di-GMP 725 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

15N: PilF 294-482, [U-15N], 471 uM; c-di-GMP 709 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

15N-Val: PilF 294-482, [U-15N]-Val, 148 uM; c-di-GMP 222 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

15N-Lys: PilF 294-482, [U-15N]-Lys, 238 uM; c-di-GMP 348 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C1-Pro_15N-Arg: PilF 294-482, [U-13C-CO]-Pro [U-15N]-Arg, 148 uM; c-di-GMP 222 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C5-Pro_15N-Leu_D2O: PilF 294-482, [U-13C; U-15N]-Pro [U-15N]-Leu, 292 uM; c-di-GMP 470 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 100%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C5-Pro_15N-Leu_H2O: PilF 294-482, [U-13C; U-15N]-Pro [U-15N]-Leu, 83 uM; c-di-GMP 125 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C1-Pro_15N-Tyr: PilF 294-482, [U-13C-CO]-Pro [U-15N]-Arg, 148 uM; c-di-GMP 222 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C15N-c-di-GMP_H2O: c-di-GMP, [U-13C; U-15N], 400 uM; PilF 294-482 509 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 7.5%; DSS 200 uM; beta-mercaptoethanol 1 mM

13C15N-c-di-GMP_D2O: c-di-GMP, [U-13C; U-15N], 400 uM; PilF 294-482 509 uM; Bis-Tris 50 mM; sodium chloride 200 mM; D2O 100%; DSS 200 uM; beta-mercaptoethanol 1 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 5.8; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC13C15Nisotropicsample_conditions_1
3D HNCO13C15Nisotropicsample_conditions_1
3D HN(CA)CO13C15Nisotropicsample_conditions_1
3D HNCA13C15Nisotropicsample_conditions_1
3D HNCACB13C15Nisotropicsample_conditions_1
3D HN(CO)CACB13C15Nisotropicsample_conditions_1
3D HBHA(CO)NH13C15Nisotropicsample_conditions_1
3D H(CCO)NH13C15Nisotropicsample_conditions_1
3D C(CO)NH13C15Nisotropicsample_conditions_1
3D HCCH-TOCSY13C15Nisotropicsample_conditions_1
2D 1H-13C HSQC aromatic13C15Nisotropicsample_conditions_1
3D 1H-13C NOESY aromatic13C15Nisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic13C15Nisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic13C15Nisotropicsample_conditions_1
2D 1H-15N HSQC15Nisotropicsample_conditions_1
3D 1H-15N NOESY15Nisotropicsample_conditions_1
2D 1H-13C HSQC aromatic13C15N-c-di-GMP_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aromatic13C15N-c-di-GMP_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic13C15N-c-di-GMP_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic13C15N-c-di-GMP_D2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromatic13C15N-c-di-GMP_D2Oisotropicsample_conditions_1
3D HCCH-COSY13C15N-c-di-GMP_D2Oisotropicsample_conditions_1
3D H(C)N13C15N-c-di-GMP_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC15N-Valisotropicsample_conditions_1
2D 1H-15N HSQC15N-Lysisotropicsample_conditions_1
2D 1H-15N HSQC13C1-Pro_15N-Tyrisotropicsample_conditions_1
1D H(NCO)13C1-Pro_15N-Tyrisotropicsample_conditions_1
2D 1H-15N HSQC13C1-Pro_15N-Argisotropicsample_conditions_1
1D H(NCO)13C1-Pro_15N-Argisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic13C5-Pro_15N-Leu_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic13C5-Pro_15N-Leu_D2Oisotropicsample_conditions_1
3D HCCH-COSY13C5-Pro_15N-Leu_D2Oisotropicsample_conditions_1
3D HCCH-TOCSY13C5-Pro_15N-Leu_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC13C5-Pro_15N-Leu_H2Oisotropicsample_conditions_1
1D H(NCO)13C5-Pro_15N-Leu_H2Oisotropicsample_conditions_1

Software:

TOPSPIN v3.5, Bruker Biospin - collection, data analysis, processing

CARA, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 950 MHz

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