BMRB Entry 34549

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34549
MolProbity Validation Chart

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Title:
NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1
Deposition date:
2020-08-06
Original release date:
2021-06-29
Authors:
Qureshi, N.; Matzel, T.; Cetiner, E.; Schnieders, S.; Jonker, H.; Schwalbe, H.; Fuertig, B.
Citation:

Citation: Qureshi, N.; Matzel, T.; Cetiner, E.; Schnieders, R.; Jonker, H.; Schwalbe, H.; Fuertig, B.. "NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs"  Nucleic Acids Res. 49, 7753-7764 (2021).
PubMed: 34223902

Assembly members:

Assembly members:
entity_1, polymer, 173 residues, 19393.109 Da.

Natural source:

Natural source:   Common Name: Vibrio vulnificus   Taxonomy ID: 672   Superkingdom: Viruses   Kingdom: not available   Genus/species: Vibrio vulnificus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pKMTX

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMETLQEGSEVKGIVKNLT DYGAFVDLGGVDGLLHITDM AWKRVKHPSEIVNVGDEILV KVLKFDRDRTRVSLGLKQLG EDPWVAIAKRYPEGHKLSGR VTNLTDYGCFVEIEEGVEGL VHVSEMDWTNKNIHPSKVVN VGDEVEVMVLEIDEERRRIS LGLKQCKANPWQS

Data sets:
Data typeCount
13C chemical shifts738
15N chemical shifts174
1H chemical shifts1199

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 173 residues - 19393.109 Da.

1   GLYALAMETGLUTHRLEUGLNGLUGLYSER
2   GLUVALLYSGLYILEVALLYSASNLEUTHR
3   ASPTYRGLYALAPHEVALASPLEUGLYGLY
4   VALASPGLYLEULEUHISILETHRASPMET
5   ALATRPLYSARGVALLYSHISPROSERGLU
6   ILEVALASNVALGLYASPGLUILELEUVAL
7   LYSVALLEULYSPHEASPARGASPARGTHR
8   ARGVALSERLEUGLYLEULYSGLNLEUGLY
9   GLUASPPROTRPVALALAILEALALYSARG
10   TYRPROGLUGLYHISLYSLEUSERGLYARG
11   VALTHRASNLEUTHRASPTYRGLYCYSPHE
12   VALGLUILEGLUGLUGLYVALGLUGLYLEU
13   VALHISVALSERGLUMETASPTRPTHRASN
14   LYSASNILEHISPROSERLYSVALVALASN
15   VALGLYASPGLUVALGLUVALMETVALLEU
16   GLUILEASPGLUGLUARGARGARGILESER
17   LEUGLYLEULYSGLNCYSLYSALAASNPRO
18   TRPGLNSER

Samples:

sample_1: rS1-D34, [U-15N], 1.3 mM; potassium phosphate 25 mM; potassium chloride 150 mM; DTT 5 mM

sample_2: rS1-D34, [U-13C; U-15N], 0.9 mM; potassium phosphate 25 mM; potassium chloride 150 mM; DTT 5 mM

sample_3: rS1-D34, [U-13C; U-15N; 60%-2H], 0.7 mM; potassium phosphate 25 mM; potassium chloride 150 mM; DTT 5 mM

sample_conditions_1: ionic strength: 208 mM; pH: 7.2; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HN(COCA)CBsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D CC(CO)NHsample_3isotropicsample_conditions_1
3D HCC(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
2D 1H-15N IPAP-HSQCsample_1isotropicsample_conditions_1
2D 1H-15N IPAP-HSQCsample_1anisotropicsample_conditions_1

Software:

TopSpin v3.x 4.x, Bruker Biospin - collection, processing

Sparky v3.114, Goddard and Kneller - chemical shift assignment, data analysis, peak picking

CYANA v3.x, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA v1.2 HJ, Linge, O'Donoghue and Nilges - refinement

TALOS-N, Shen and Bax - data analysis

PALES, Zweckstetter and Bax - data analysis

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE 700 MHz
  • Bruker AVANCE 800 MHz
  • Bruker AVANCE 900 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