BMRB Entry 18788

Name: Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+
Published: 2013-02-21

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PDB ID: 2m00
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18788
MolProbity Validation Chart

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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:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
staph_nuc_E43S: ATSTKKLHKEPATLIKAIDG DTVKLMYKGQPMTFRLLLVD TPSTKHPKKGVEKYGPEASA FTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVN EALVRQGLAKVAYVYKPNNT HEQLLRKSEAQAKKEKLNIW SEDNADSGQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	567
15N chemical shifts	138
1H chemical shifts	920

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	staph_nuc_E43S	1

Entities:

Entity 1, staph_nuc_E43S 149 residues - 16776.459 Da.

1

ALA

THR

SER

THR

LYS

LEU

HIS

LYS

GLU

2

PRO

ALA

THR

LEU

ILE

LYS

ALA

ILE

ASP

GLY

3

ASP

THR

VAL

LYS

LEU

MET

TYR

LYS

GLY

GLN

4

PRO

MET

THR

PHE

ARG

LEU

VAL

ASP

5

THR

PRO

SER

THR

LYS

HIS

PRO

LYS

GLY

6

VAL

GLU

LYS

TYR

GLY

PRO

GLU

ALA

SER

ALA

7

PHE

THR

LYS

MET

VAL

GLU

ASN

ALA

LYS

8

LYS

ILE

GLU

VAL

GLU

PHE

ASP

LYS

GLY

GLN

9

ARG

THR

ASP

LYS

TYR

GLY

ARG

GLY

LEU

ALA

10

TYR

ILE

TYR

ALA

ASP

GLY

LYS

MET

VAL

ASN

11

GLU

ALA

LEU

VAL

ARG

GLN

GLY

LEU

ALA

LYS

12

VAL

ALA

TYR

VAL

TYR

LYS

PRO

ASN

THR

13

HIS

GLU

GLN

LEU

ARG

LYS

SER

GLU

ALA

14

GLN

ALA

LYS

GLU

LYS

LEU

ASN

ILE

TRP

15

SER

GLU

ASP

ASN

ALA

ASP

SER

GLY

GLN

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHANH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_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	1A2T 1A2U 1A3T 1A3U 1A3V 1AEX 1ENA 1ENC 1EY0 1EY4 1EY5 1EY6 1EY7 1EY8 1EY9 1EYD 1EZ8 1F2M 1F2Y 1F2Z 1JOK 1JOO 1JOQ 1JOR 1KAA 1KAB 1NSN 1NUC 1RKN 1SNC 1SNM 1SNO 1SNP 1SNQ 1STA 1STB 1STG 1STH 1STN 1STY 1SYC 1SYD 1SYE 1SYF 1SYG 1U9R 2ENB 2EXZ 2EY1 2EY2 2EY5 2EY6 2EYF 2EYH 2EYJ 2EYL 2EYM 2EYO 2EYP 2F0D 2F0E 2F0F 2F0G 2F0H 2F0I 2F0J 2F0K 2F0L 2F0M 2F0N 2F0O 2F0P 2F0Q 2F0S 2F0T 2F3V 2F3W 2KHS 2KQ3 2LKV 2M00 2NUC 2OXP 2PW5 2PW7 2PYK 2PZT 2PZU 2PZW 2RKS 2SNM 2SOB 3D6C 3DMU 3NUC 4G57 4H7B 4ID6 4K14 4K5X 4K6D 4K8I 4K8J 4WOR 5NUC
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