BMRB Entry 18320

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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/BMR18320
MolProbity Validation Chart

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Title:
Solution Structures of RadA intein from Pyrococcus horikoshii
Deposition date:
2012-03-09
Original release date:
2012-05-15
Authors:
Oeemig, Jesper; Zhou, Dongwen; Kajander, Tommi; Wlodawer, Alexander; Iwai, Hideo
Citation:

Citation: Oeemig, Jesper; Zhou, Dongwen; Kajander, Tommi; Wlodawer, Alexander; Iwai, Hideo. "NMR and crystal structures of the Pyrococcus horikoshii RadA intein guide a strategy for engineering a highly efficient and promiscuous intein."  J. Mol. Biol. 421, 85-99 (2012).
PubMed: 22560994

Assembly members:

Assembly members:
PhoRadA_intein, polymer, 174 residues, 19918.725 Da.

Natural source:

Natural source:   Common Name: euryarchaeotes   Taxonomy ID: 70601   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus Pyrococcus horikoshii

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pKRRSF15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PhoRadA_intein: AFARDTEVYYENDTVPHMES IEEMYSKYASMNGELPFDNG YAVPLDNVFVYTLDIASGEI KKTRASYIYREKVEKLIEIK LSSGYSLKVTPSHPVLLFRD GLQWVPAAEVKPGDVVVGVR EEVLRRRIISKGELEFHEVS SVRIIDYNNWVYDLVIPETH NFIAPNGLVLHNAQ

Data sets:
Data typeCount
13C chemical shifts708
15N chemical shifts162
1H chemical shifts1204

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PhoRadA intein1

Entities:

Entity 1, PhoRadA intein 174 residues - 19918.725 Da.

Residue 1-172 PhoRadA intein. Residue 173-174 is C-extein sequence

1   ALAPHEALAARGASPTHRGLUVALTYRTYR
2   GLUASNASPTHRVALPROHISMETGLUSER
3   ILEGLUGLUMETTYRSERLYSTYRALASER
4   METASNGLYGLULEUPROPHEASPASNGLY
5   TYRALAVALPROLEUASPASNVALPHEVAL
6   TYRTHRLEUASPILEALASERGLYGLUILE
7   LYSLYSTHRARGALASERTYRILETYRARG
8   GLULYSVALGLULYSLEUILEGLUILELYS
9   LEUSERSERGLYTYRSERLEULYSVALTHR
10   PROSERHISPROVALLEULEUPHEARGASP
11   GLYLEUGLNTRPVALPROALAALAGLUVAL
12   LYSPROGLYASPVALVALVALGLYVALARG
13   GLUGLUVALLEUARGARGARGILEILESER
14   LYSGLYGLULEUGLUPHEHISGLUVALSER
15   SERVALARGILEILEASPTYRASNASNTRP
16   VALTYRASPLEUVALILEPROGLUTHRHIS
17   ASNPHEILEALAPROASNGLYLEUVALLEU
18   HISASNALAGLN

Samples:

sample_1: PhoRadA intein, [U-99% 13C; U-99% 15N], 0.4 mM; sodium phosphate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_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 HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HCACOsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
intraHNCAsample_1isotropicsample_conditions_1
HBCBCGCDHDsample_1isotropicsample_conditions_1
HBCBCGCDCEHEsample_1isotropicsample_conditions_1

Software:

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

VNMRJ v2.2, Varian - collection

NMRPipe v5.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CING, Geerten W. Vuister - Structure validation

CcpNMR v2.2, CCPN - data analysis

TALOS vTALOS+, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAA29335
REF WP_048053072
SP O58001
AlphaFold O58001

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