BMRB Entry 11030

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11030
MolProbity Validation Chart

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Title:
Solution Structure of the N-terminal SAP Domain of SUMO E3 Ligases from Oryza sativa
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 1-105, polymer, 110 residues, 12388.231 Da.

Natural source:

Natural source:   Common Name: Oryza sativa   Taxonomy ID: 39947   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Oryza sativa

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Siz1 1-105: GSHMASADLVSSCKDKLAYF RIKELKDILNQLGLPKQGKK QDLIDRVLALLTDEQGQRHH GWGRKNSLTKEAVAKIVDDT YRKMQIQCAPDLATRSHSGS DFSFRPIEEA

Data sets:
Data typeCount
13C chemical shifts927
15N chemical shifts244
1H chemical shifts1468

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Siz1 1-1051

Entities:

Entity 1, Siz1 1-105 110 residues - 12388.231 Da.

Residues (-5)-1 represent a non-native sequence from affinity tag.

1   GLYSERHISMETALASERALAASPLEUVAL
2   SERSERCYSLYSASPLYSLEUALATYRPHE
3   ARGILELYSGLULEULYSASPILELEUASN
4   GLNLEUGLYLEUPROLYSGLNGLYLYSLYS
5   GLNASPLEUILEASPARGVALLEUALALEU
6   LEUTHRASPGLUGLNGLYGLNARGHISHIS
7   GLYTRPGLYARGLYSASNSERLEUTHRLYS
8   GLUALAVALALALYSILEVALASPASPTHR
9   TYRARGLYSMETGLNILEGLNCYSALAPRO
10   ASPLEUALATHRARGSERHISSERGLYSER
11   ASPPHESERPHEARGPROILEGLUGLUALA

Samples:

13C_15N_in_10%_D2O: Siz1 1-105, [U-13C; U-15N], 0.7 mM; potassium phosphate 20 mM; sodium chloride 300 mM; DTT 2 mM; H2O 92%; D2O 8%

13C_15N_in_100%_D2O: Siz1 1-105, [U-13C; U-15N], 0.7 mM; potassium phosphate 20 mM; sodium chloride 300 mM; DTT 2 mM; D2O 100%

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

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC13C_15N_in_10%_D2OisotropicpH_6.1
3D 1H-15N NOESY13C_15N_in_10%_D2OisotropicpH_6.1
3D HNCO13C_15N_in_10%_D2OisotropicpH_6.1
3D HNCA13C_15N_in_10%_D2OisotropicpH_6.1
3D CBCA(CO)NH13C_15N_in_10%_D2OisotropicpH_6.1
3D 13C-edited 1H-15N NOESY13C_15N_in_10%_D2OisotropicpH_6.1
2D 1H-13C HSQC13C_15N_in_100%_D2OisotropicpH_6.1
3D HCCH-TOCSY13C_15N_in_100%_D2OisotropicpH_6.1
4D 1H-13C NOESY13C_15N_in_100%_D2OisotropicpH_6.1
3D HCABGCO13C_15N_in_100%_D2OisotropicpH_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

Related Database Links:

PDB
DBJ BAF16431 BAG97182 BAS92058
GB AAT39226 EEC78434 EEE62174
REF NP_001054517
SP Q6L4L4
AlphaFold Q6L4L4

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