BMRB Entry 50001

Name: Solution structure of protein ARR_CleD in complex with c-di-GMP
Published: 2020-09-21

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PDB ID: 6sft
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50001
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of protein ARR_CleD in complex with c-di-GMP

Deposition date:

2019-08-16

Original release date:

2020-09-21

Authors:

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

Citation:

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).
PubMed: 32611811

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SKPREWVEAVAYVGPDRRRF NSADYKGPRKRKADAS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
- heteronuclear_Rex_list_1
order_parameters
- order_parameter_list_1

Data type	Count
13C chemical shifts	125
15N chemical shifts	40
1H chemical shifts	267
T1 relaxation values	30
T2 relaxation values	60
heteronuclear NOE values	30
order parameters	30

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ARR_CleD	1
2	c-di-GMP, 1	2
3	c-di-GMP, 2	2

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

SER

LYS

PRO

ARG

GLU

TRP

VAL

GLU

ALA

VAL

2

ALA

TYR

VAL

GLY

PRO

ASP

ARG

PHE

3

ASN

SER

ALA

ASP

TYR

LYS

GLY

PRO

ARG

LYS

4

ARG

LYS

ALA

ASP

ALA

SER

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N NH2 TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N NH2 NOESY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D CBCANH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
2D 1H-15N NOE without saturation	sample_1	isotropic	sample_conditions_1
2D 1H-15N NOE with saturation	sample_1	isotropic	sample_conditions_1
3D 1H-15N t1 interleaved	sample_1	isotropic	sample_conditions_1
3D 1H-15N t2 interleaved	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC without 15 decoupling	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC without 15N decoupling	sample_3	anisotropic	sample_conditions_2
2D HN(CO)CA without decoupling	sample_2	isotropic	sample_conditions_1
2D HN(CO)CA without decoupling	sample_3	anisotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_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