BMRB Entry 11029

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PDB ID: 2rnn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11029
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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 the N-terminal SAP Domain of SUMO E3 Ligases from Saccharomyces cerevisiae

Deposition date:

2008-01-29

Original release date:

2008-11-11

Authors:

Suzuki, Rintaro; Shindo, Heisaburo; Tase, Akira; Yamazaki, Toshimasa

Citation:

Citation: Suzuki, Rintaro; Shindo, Heisaburo; Tase, Akira; Kikuchi, Yoshiko; Shimizu, Mitsuhiro; Yamazaki, Toshimasa. "Solution Structures and DNA Binding Properties of the N-terminal SAP Domains of SUMO E3 Ligases from Saccharomyces cerevisiae and Oryza sativa." Proteins 75, 336-347 (2008).
PubMed: 18831036

Assembly members:

Assembly members:
Siz1 1-111, polymer, 114 residues, 13249.319 Da.

Natural source:

Natural source: Common Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-28b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Siz1 1-111: GSHMINLEDYWEDETPGPDR EPTNELRNEVEETITLMELL KVSELKDICRSVSFPVSGRK AVLQDLIRNFLQNALVVGKS DPYRVQAVKFLIERIRKNEP LPVYKDLWNALRKG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	505
15N chemical shifts	125
1H chemical shifts	861

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Siz1 1-111	1

Entities:

Entity 1, Siz1 1-111 114 residues - 13249.319 Da.

Residues (-3)-(-1) represent a non-native sequence from affinity tag.

1

GLY

SER

HIS

MET

ILE

ASN

LEU

GLU

ASP

TYR

2

TRP

GLU

ASP

GLU

THR

PRO

GLY

PRO

ASP

ARG

3

GLU

PRO

THR

ASN

GLU

LEU

ARG

ASN

GLU

VAL

4

GLU

THR

ILE

THR

LEU

MET

GLU

LEU

5

LYS

VAL

SER

GLU

LEU

LYS

ASP

ILE

CYS

ARG

6

SER

VAL

SER

PHE

PRO

VAL

SER

GLY

ARG

LYS

7

ALA

VAL

LEU

GLN

ASP

LEU

ILE

ARG

ASN

PHE

8

LEU

GLN

ASN

ALA

LEU

VAL

GLY

LYS

SER

9

ASP

PRO

TYR

ARG

VAL

GLN

ALA

VAL

LYS

PHE

10

LEU

ILE

GLU

ARG

ILE

ARG

LYS

ASN

GLU

PRO

11

LEU

PRO

VAL

TYR

LYS

ASP

LEU

TRP

ASN

ALA

12

LEU

ARG

LYS

GLY

Samples:

15N_in_8%_D2O: Siz1 1-111, [U-15N], 0.55 mM; potassium phosphate 20 mM; sodium chloride 300 mM; DTT 3 mM; H2O 92%; D2O 8%

13C_15N_in_8%_D2O: Siz1 1-111, [U-13C; U-15N], 0.6 mM; potassium phosphate 20 mM; sodium chloride 300 mM; DTT 3 mM; H2O 92%; D2O 8%

13C_15N_in_100%_D2O: Siz1 1-111, [U-13C; U-15N], 0.69 mM; potassium phosphate 20 mM; sodium chloride 300 mM; DTT 3 mM; D2O 100%

pH_6.1: pH: 6.1; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N_in_8%_D2O	isotropic	pH_6.1
3D 1H-15N NOESY	15N_in_8%_D2O	isotropic	pH_6.1
2D 1H-15N HSQC	13C_15N_in_8%_D2O	isotropic	pH_6.1
3D HNCO	13C_15N_in_8%_D2O	isotropic	pH_6.1
3D HNCA	13C_15N_in_8%_D2O	isotropic	pH_6.1
3D CBCA(CO)NH	13C_15N_in_8%_D2O	isotropic	pH_6.1
3D 13C-edited 1H-15N NOESY	13C_15N_in_8%_D2O	isotropic	pH_6.1
2D 1H-13C HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.1
3D HCCH-TOCSY	13C_15N_in_100%_D2O	isotropic	pH_6.1
4D 1H-13C NOESY	13C_15N_in_100%_D2O	isotropic	pH_6.1

Software:

xwinnmr v3.1, Bruker Biospin - collection

NMRPipe vreleased at Feb 10, 2006, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

PIPP v4.3.6, Garrett - chemical shift assignment, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

AQUA v3.2, Rullmann, Doreleijers and Kaptein - data analysis

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker DMX 750 MHz

PDB	2RNN
DBJ	GAA22629
GB	AAB64849 AHY75365 AJP38091 AJU58213 AJU58906
REF	NP_010697
SP	Q04195
TPG	DAA12251
AlphaFold	Q04195