BMRB Entry 19039

Name: NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8
Published: 2014-02-24

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PDB ID: 2m57
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19039
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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:

NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8

Deposition date:

2013-02-15

Original release date:

2014-02-24

Authors:

Pechlaner, Maria; Donghi, Daniela; Zelenay, Veronika; Sigel, Roland K. O.

Citation:

Citation: Pechlaner, Maria; Donghi, Daniela; Zelenay, Veronika; Sigel, Roland K. O.. "Acid-base equilibria near neutral pH in the catalytic triad and the bulge of domain 5 of a bacterial group II intron" .

Assembly members:

Assembly members:
RNA_(35-MER), polymer, 35 residues, 11268.784 Da.

Natural source:

Natural source: Common Name: Azotobacter vinelandii Taxonomy ID: 354 Superkingdom: Bacteria Kingdom: not available Genus/species: Azotobacter vinelandii

Experimental source:

Experimental source: Production method: cell free synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(35-MER): GGAGCCGUAUGCGGUAGUUC CGCACGUACGGAUCU

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	216
15N chemical shifts	95
1H chemical shifts	569

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (35-MER)	1

Entities:

Entity 1, RNA (35-MER) 35 residues - 11268.784 Da.

The sequence corresponds to residues 1836 to 1870 from group II intron 5 of A. vinelandii (numbering includes the open reading frame).

1

G

A

G

C

G

U

A

U

2

G

C

G

U

A

G

U

C

3

C

G

C

A

C

G

U

A

C

G

4

G

A

U

C

U

Samples:

AvD5_wt_d2o: RNA (35-MER)0.5 – 1 mM; potassium chloride 60 mM; EDTA 10 uM

AvD5_wt_h2o: RNA (35-MER)0.5 – 1 mM; potassium chloride 60 mM; EDTA 10 uM

AvD5_lab_d2o: RNA (35-MER), [100% 13C; 100% 15N], 0.5 – 1 mM; potassium chloride 60 mM; EDTA 10 uM

AvD5_lab_h2o: RNA (35-MER), [100% 13C; 100% 15N], 0.5 – 1 mM; potassium chloride 60 mM; EDTA 10 uM

AvD5_deut_d2o: RNA (35-MER), [3',4',5',5'',5]-100% 2D, 0.5 – 1 mM; potassium chloride 60 mM; EDTA 10 uM

300K_d2o_pH7.8: ionic strength: 60 mM; pD: 7.8; pressure: 1 atm; temperature: 300 K

275K_h2o_pH7.8: ionic strength: 60 mM; pH: 7.8; pressure: 1 atm; temperature: 275 K

300K_d2o_pH5.2: ionic strength: 60 mM; pD: 5.2; pressure: 1 atm; temperature: 300 K

300K_d2o_pH6.7: ionic strength: 60 mM; pD: 6.7; pressure: 1 atm; temperature: 300 K

275K_h2o_pH5.2: ionic strength: 60 mM; pH: 5.2; pressure: 1 atm; temperature: 275 K

275K_h2o_pH6.7: ionic strength: 60 mM; pH: 6.7; pressure: 1 atm; temperature: 275 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	AvD5_wt_d2o	isotropic	300K_d2o_pH7.8
2D 1H-1H NOESY	AvD5_deut_d2o	isotropic	300K_d2o_pH7.8
2D 1H-1H NOESY	AvD5_wt_h2o	isotropic	275K_h2o_pH7.8
2D 1H-1H TOCSY	AvD5_wt_d2o	isotropic	300K_d2o_pH7.8
2D 1H-15N HSQC	AvD5_lab_h2o	isotropic	275K_h2o_pH7.8
2D 1H-13C HSQC aromatic	AvD5_lab_d2o	isotropic	300K_d2o_pH7.8
2D 1H-13C HSQC aliphatic	AvD5_lab_d2o	isotropic	300K_d2o_pH7.8
2D JNN HNN COSY	AvD5_lab_h2o	isotropic	275K_h2o_pH7.8
2D 1H-1H NOESY	AvD5_wt_d2o	isotropic	300K_d2o_pH5.2
2D 1H-1H NOESY	AvD5_wt_d2o	isotropic	300K_d2o_pH6.7
2D 1H-1H NOESY	AvD5_wt_h2o	isotropic	275K_h2o_pH5.2
2D 1H-1H NOESY	AvD5_wt_h2o	isotropic	275K_h2o_pH6.7
2D 1H-13C HSQC aromatic	AvD5_lab_d2o	isotropic	300K_d2o_pH5.2
2D 1H-13C HSQC aromatic	AvD5_lab_d2o	isotropic	300K_d2o_pH6.7
2D 1H-13C HSQC aliphatic	AvD5_lab_d2o	isotropic	300K_d2o_pH6.7
2D 1H-15N HSQC	AvD5_lab_h2o	isotropic	275K_h2o_pH5.2
2D 1H-15N HSQC	AvD5_lab_h2o	isotropic	275K_h2o_pH6.7
2D JNN HNN COSY	AvD5_lab_h2o	isotropic	275K_h2o_pH5.2
2D JNN HNN COSY	AvD5_lab_h2o	isotropic	275K_h2o_pH6.7

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

X-PLOR NIH v2.3, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN v3.0.a, Bruker Biospin - data analysis, processing

CURVES, Lavery - data analysis

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz