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BMRB: 18788

2M00

Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+

Authors

Xie, T., Feng, Y., Shan, L., Wang, J.

Assembly

staphylococcal nuclease E43S mutant

Entity

1. staphylococcal nuclease E43S mutant (polymer, Thiol state: not present), 149 monomers, 16745.04 Da Detail

ATSTKKLHKE PATLIKAIDG DTVKLMYKGQ PMTFRLLLVD TPSTKHPKKG VEKYGPEASA FTKKMVENAK KIEVEFDKGQ RTDKYGRGLA YIYADGKMVN EALVRQGLAK VAYVYKPNNT HEQLLRKSEA QAKKEKLNIW SEDNADSGQ

Formula weight

16745.04 Da

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.3 %, Completeness: 84.4 %, Completeness (bb): 88.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (1502 of 1780)	83.5 % (783 of 938)	84.5 % (580 of 686)	89.1 % (139 of 156)
Backbone	88.4 % (780 of 882)	87.7 % (265 of 302)	89.0 % (389 of 437)	88.1 % (126 of 143)
Sidechain	81.5 % (845 of 1037)	81.4 % (518 of 636)	80.9 % (314 of 388)	100.0 % (13 of 13)
Aromatic	72.7 % (80 of 110)	74.5 % (41 of 55)	70.4 % (38 of 54)	100.0 % (1 of 1)
Methyl	88.2 % (134 of 152)	86.8 % (66 of 76)	89.5 % (68 of 76)

1. staph nuc E43S

ATSTKKLHKE PATLIKAIDG DTVKLMYKGQ PMTFRLLLVD TPSTKHPKKG VEKYGPEASA FTKKMVENAK KIEVEFDKGQ RTDKYGRGLA YIYADGKMVN EALVRQGLAK VAYVYKPNNT HEQLLRKSEA QAKKEKLNIW SEDNADSGQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	staph_nuc_E43S	[U-13C; U-15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	CdCl2	natural abundance	10 mM
5	sodium azide	natural abundance	0.2% w/v
6	8-mer ssDNA(5'-CACTTCAT-3')	natural abundance	1.5 ~ 2.25 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 5 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 5 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.29 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M00, Strand ID: A Detail

Release date

2013-02-20

Citation

Modeling of the [E43S]SNase-ssDNA-Cd(2+) complex: structural insight into the action of nuclease on ssDNA
Xie, T., Feng, Y., Shan, L., Wang, J.
Arch. Biochem. Biophys. (2013), 532, 103-113, PubMed 23416741 , DOI 10.1016/j.abb.2013.02.003 , Abstract

Related entities 1. staphylococcal nuclease E43S mutant, : 1 : 51 : 84 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC