BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 50001

Title: Solution structure of protein ARR_CleD in complex with c-di-GMP   PubMed: 32611811

Deposition date: 2019-08-16 Original release date: 2020-09-21

Authors: Habazettl, Judith; Grzesiek, Stephan; Hee, Chee-Seng

Citation: Hee, Chee-Seng; Habazettl, Judith; Schmutz, Christoph; Schirmer, Tilman; Jenal, Urs; Grzesiek, Stephan. "Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP"  Proc. Natl. Acad. Sci. U.S.A. 117, 17211-17220 (2020).

Assembly members:
entity_1, polymer, 36 residues, Formula weight is not available
entity_C2E, non-polymer, 690.411 Da.

Natural source:   Common Name: Caulobacter crescentus   Taxonomy ID: 565050   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Caulobacter crescentus

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

Entity Sequences (FASTA):
entity_1: SKPREWVEAVAYVGPDRRRF NSADYKGPRKRKADAS

Data sets:
Data typeCount
13C chemical shifts125
15N chemical shifts40
1H chemical shifts267
T1 relaxation values30
T2 relaxation values60
heteronuclear NOE values30
order parameters30

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ARR_CleD1
2c-di-GMP, 12
3c-di-GMP, 22

Entities:

Entity 1, ARR_CleD 36 residues - Formula weight is not available

This is the arginine rich region of CleD and binds ci-di-GMP.

1   SERLYSPROARGGLUTRPVALGLUALAVAL
2   ALATYRVALGLYPROASPARGARGARGPHE
3   ASNSERALAASPTYRLYSGLYPROARGLYS
4   ARGLYSALAASPALASER

Entity 2, c-di-GMP, 1 - C20 H24 N10 O14 P2 - 690.411 Da.

1   C2E

Samples:

sample_1: ARR_CleD, [U-98% 15N], 1 mM; C2E 3 mM; sodium chloride 100 mM; sodium phosphate 20 mM; sodium azide 0.02 v/v; magnsesium chloride 2 mM

sample_2: ARR_CleD, [U-98% 13C; U-98% 15N], 1 mM; C2E 3 mM; sodium chloride 100 mM; sodium phosphate 20 mM; sodium azide 0.02 v/v; magnesium chloride 2 mM

sample_3: ARR_CleD, [U-99% 13C; U-99% 15N], 0.6 mM; C2E 1.8 mM; sodium chloride 66.66 mM; sodium phosphate 13.33 mM; mgnesium chloride 1.33 mM; Pf1 phage 9 mg/mL

sample_conditions_1: ionic strength: 0.47 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.31 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlysample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N NH2 TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N NH2 NOESYsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D CBCANHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
2D 1H-15N NOE without saturationsample_1isotropicsample_conditions_1
2D 1H-15N NOE with saturationsample_1isotropicsample_conditions_1
3D 1H-15N t1 interleavedsample_1isotropicsample_conditions_1
3D 1H-15N t2 interleavedsample_1isotropicsample_conditions_1
2D 1H-15N HSQC without 15 decouplingsample_2isotropicsample_conditions_1
2D 1H-15N HSQC without 15N decouplingsample_3anisotropicsample_conditions_2
2D HN(CO)CA without decouplingsample_2isotropicsample_conditions_1
2D HN(CO)CA without decouplingsample_3anisotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

Bruker, Bruker Biospin - recording of spectra

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

MATLAB, MathWorks - fit of relaxation data

ModelFree, Palmer - aanalyze the relaxation data and fits them to different models

PIPP, Garrett - peak picking

NMR spectrometers:

  • Bruker Uniform NMR System 900 MHz
  • Bruker Uniform NMR System 800 MHz
  • Bruker Uniform NMR System 600 MHz

Related Database Links:

UniProtKB A0A0H3CCM2

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts