BMRB Entry 18788

Title:
Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+
Deposition date:
2012-10-14
Original release date:
2013-02-21
Authors:
Xie, Tao; Feng, Yingang; Shan, Lu; Wang, Jinfeng
Citation:

Citation: Xie, Tao; Feng, Yingang; Shan, Lu; Wang, Jinfeng. "Modeling of the [E43S]SNase-ssDNA-Cd(2+) complex: structural insight into the action of nuclease on ssDNA."  Arch. Biochem. Biophys. 532, 103-113 (2013).
PubMed: 23416741

Assembly members:

Assembly members:
staph_nuc_E43S, polymer, 149 residues, 16776.459 Da.

Natural source:

Natural source:   Common Name: Staphylococcus aureus   Taxonomy ID: 1280   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus aureus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-3d

Data sets:
Data typeCount
13C chemical shifts567
15N chemical shifts138
1H chemical shifts920

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1staph_nuc_E43S1

Entities:

Entity 1, staph_nuc_E43S 149 residues - 16776.459 Da.

1   ALATHRSERTHRLYSLYSLEUHISLYSGLU
2   PROALATHRLEUILELYSALAILEASPGLY
3   ASPTHRVALLYSLEUMETTYRLYSGLYGLN
4   PROMETTHRPHEARGLEULEULEUVALASP
5   THRPROSERTHRLYSHISPROLYSLYSGLY
6   VALGLULYSTYRGLYPROGLUALASERALA
7   PHETHRLYSLYSMETVALGLUASNALALYS
8   LYSILEGLUVALGLUPHEASPLYSGLYGLN
9   ARGTHRASPLYSTYRGLYARGGLYLEUALA
10   TYRILETYRALAASPGLYLYSMETVALASN
11   GLUALALEUVALARGGLNGLYLEUALALYS
12   VALALATYRVALTYRLYSPROASNASNTHR
13   HISGLUGLNLEULEUARGLYSSERGLUALA
14   GLNALALYSLYSGLULYSLEUASNILETRP
15   SERGLUASPASNALAASPSERGLYGLN

Samples:

sample_1: staph_nuc_E43S, [U-13C; U-15N], 1.0 – 1.5 mM; sodium phosphate 50 mM; potassium chloride 150 mM; CdCl2 10 mM; sodium azide 0.2% w/v; 8-mer ssDNA(5'-CACTTCAT-3')1.5 – 2.25 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 210 mM; pH: 6.6; pressure: 1 atm; temperature: 305 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, processing

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

NMR spectrometers:

  • Bruker DMX 600 MHz

Related Database Links:

BMRB 16585 1704 17718 18013 1874 1875 1876 1877 1878 4010 4052 4053
PDB
DBJ BAB41979 BAB56977 BAB94634 BAF67032 BAF77694
EMBL CAA24594 CAG39855 CAG42530 CAI80436 CAQ49298
GB AAC14660 AAW36415 ABD22328 ABD29945 ABE02272
PRF 1109959A 710414A
REF WP_000141556 WP_000141557 WP_001548082 WP_001566557 WP_001574556
SP P00644 Q5HHM4 Q6GB41 Q6GIK1 Q7A6P2
AlphaFold P00644 Q5HHM4 Q6GB41 Q6GIK1 Q7A6P2

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks