BMRB Entry 6076

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PDB ID: 1r7w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR6076
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Loop B RNAs from the Stem-Loop IV domain of the Enterovirus Internal Ribosome Entry Site with a Six-nucleotide Bulge AUCCCU

Deposition date:

2004-01-13

Original release date:

2004-06-30

Authors:

Du, Z.; Ulyanov, N.; Yu, J.; James, T.

Citation:

Citation: Du, Z.; Ulyanov, N.; Yu, J.; Andino, R.; James, T.. "NMR Structures of Loop B RNAs from the Stem-Loop IV Domain of the Enterovirus Internal Ribosome Entry Site: A Single C to U Substitution Drastically Changes the Shape and Flexibility of RNA" Biochemistry 43, 5757-5771 (2004).
PubMed: 15134450

Assembly members:

Assembly members:

Natural source:

Natural source: Common Name: Enterovirus poliovirus Taxonomy ID: 138953 Superkingdom: Viruses Kingdom: not available Genus/species: Enterovirus poliovirus

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1
- chemical_shift_set_2

Data type	Count
13C chemical shifts	226
15N chemical shifts	34
1H chemical shifts	406

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID

Entities:

Samples:

sample_1: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; H2O 90%; D2O 10%

sample_2: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_3: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N], 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_4: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N]-A, U, 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_5: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N]-C, 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%

sample_6: RNA FRAGMENT OF DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES, [U-13C; U-15N], 1.0 – 2.0 mM; NaCl 25 mM; sodium phosphate buffer 25 mM; D2O 100%; C12E6/N-HEXANOL MIXTURE (MOLAR RATIO 0.64) 5%

sample_cond_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_cond_2: ionic strength: 50 mM; pH*: 6.5; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
DQF-COSY	not available	not available	not available
3D 13C-separated NOESY	not available	not available	not available
1H-13C CONSTANT TIME HSQC	not available	not available	not available

Software:

VNMR v6.1 - collection

NMRPipe v2.1 - processing

MARDIGRAS v3.2 - iterative matrix relaxation

DYANA v1.5 - refinement

AMBER v7 - refinement

NMR spectrometers:

Varian INOVA 600 MHz