BMRB Entry 15693

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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/BMR15693
MolProbity Validation Chart

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Title:
Solution structure of Human Pax8 Paired Box Domain
Deposition date:
2008-03-26
Original release date:
2008-09-22
Authors:
Codutti, Luca; Esposito, Gennaro; Corazza, Alessandra; Fogolari, Federico; Tell, Gianluca; Vascotto, Carlo; van Ingen, Hugo; Boelens, Rolf; Viglino, Paolo; Quadrifoglio, Franco
Citation:

Citation: Codutti, Luca; van Ingen, Hugo; Vascotto, Carlo; Fogolari, Federico; Corazza, Alessandra; Tell, Gianluca; Quadrifoglio, Franco; Viglino, Paolo; Boelens, Rolf; Esposito, Gennaro. "The solution structure of DNA-free Pax-8 Paired Box domain accounts for redox regulation of transcriptional activity in Pax protein family"  J. Biol. Chem. 283, 33321-33328 (2008).
PubMed: 18829450

Assembly members:

Assembly members:
Pax8_Paired_Box_Domain, polymer, 159 residues, 17416.87 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pIVEX2.3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Pax8_Paired_Box_Domain: MPHNSIRSGHGGLNQLGGAF VNGRPLPEVVRQRIVDLAHQ GVRPCDISRQLRVSHGCVSK ILGRYYETGSIRPGVIGGSK PKVATPKVVEKIGDYKRQNP TMFAWEIRDRLLAEGVCDND TVPSVSSINRIIRTKVQQPF NLPMDSGAPGGGSHHHHHH

Data sets:
Data typeCount
13C chemical shifts558
15N chemical shifts151
1H chemical shifts903

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Pax8 PAIRED1

Entities:

Entity 1, Pax8 PAIRED 159 residues - 17416.87 Da.

1   METPROHISASNSERILEARGSERGLYHIS
2   GLYGLYLEUASNGLNLEUGLYGLYALAPHE
3   VALASNGLYARGPROLEUPROGLUVALVAL
4   ARGGLNARGILEVALASPLEUALAHISGLN
5   GLYVALARGPROCYSASPILESERARGGLN
6   LEUARGVALSERHISGLYCYSVALSERLYS
7   ILELEUGLYARGTYRTYRGLUTHRGLYSER
8   ILEARGPROGLYVALILEGLYGLYSERLYS
9   PROLYSVALALATHRPROLYSVALVALGLU
10   LYSILEGLYASPTYRLYSARGGLNASNPRO
11   THRMETPHEALATRPGLUILEARGASPARG
12   LEULEUALAGLUGLYVALCYSASPASNASP
13   THRVALPROSERVALSERSERILEASNARG
14   ILEILEARGTHRLYSVALGLNGLNPROPHE
15   ASNLEUPROMETASPSERGLYALAPROGLY
16   GLYGLYSERHISHISHISHISHISHIS

Samples:

sample_1: Pax8 Paired Box Domain, [U-100% 13C; U-100% 15N], 0.9 ± 0.1 mM; DSS 40 ± 5 uM; sodium phosphate 50 ± 5 mM; sodium azide 0.1 ± 0.05 %; DTT, [U-100% 2H], 15 ± 2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 298.00 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC CTsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1

Software:

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

TALOS v(NMR-Pipe 3.5), Cornilescu, Delaglio and Bax - data analysis

ProcheckNMR v3.4, Laskowski and MacArthur - validation

TOPSPIN v1.3, Bruker Biospin - collection, processing

CARA v1.8.4, Rochus Keller - chemical shift assignment, data analysis, peak picking

DISCOVER v2.98, Accelrys Software Inc. - refinement

AQUA v3.2, Rullmann, Doreleijers and Kaptein - validation

WhatIF, Vriend - validation

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 2 750 MHz

Related Database Links:

PDB
DBJ BAF84880 BAI46656
EMBL CAA40725 CAA58571 CAA58572 CAA63930 CAA67904
GB AAA03539 AAB34216 AAB34217 AAB34218 AAH01060
REF NP_001003248 NP_001126820 NP_001128942 NP_003457 NP_035170
SP P47240 P51974 Q00288 Q06710 Q5R9M8
AlphaFold P47240 P51974 Q00288 Q06710 Q5R9M8

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