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Biological Magnetic Resonance Data Bank


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BMRB Entry 18653

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18653
MolProbity Validation Chart

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Title: Solution Structure of Bacterial Intein-Like domain from Clostridium thermocellum   PubMed: 23621571

Deposition date: 2012-08-09 Original release date: 2013-05-06

Authors: Aranko, A. Sesilja; Oeemig, Jesper; Iwai, Hideo

Citation: Aranko, A. Sesilja; Oeemig, Jesper; Iwai, Hideo. "Structural basis for protein trans-splicing by a bacterial intein-like domain - protein ligation without nucleophilic side chains."  FEBS J. 280, 3256-3269 (2013).

Assembly members:
CthBIL4, polymer, 138 residues, 15297.629 Da.

Natural source:   Common Name: Clostridium thermocellum   Taxonomy ID: 1515   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Clostridium thermocellum

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

Entity Sequences (FASTA):
CthBIL4: SMKAFVAGTMILTATGLVAI ENIKAGDKVIATNPETFEVA EKTVLETYVRETTELLHLTI GGEVIKTTFDHPFYVKDVGF VEAGKLQVGDKLLDSRGNVL VVEEKKLEIADKPVKVYNFK VDDFHTYHVGDNEVLVHN

Data sets:
Data typeCount
13C chemical shifts607
15N chemical shifts139
1H chemical shifts991

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Bacterial Intein-Like domain from Clostridium thermocellum1

Entities:

Entity 1, Bacterial Intein-Like domain from Clostridium thermocellum 138 residues - 15297.629 Da.

S-3 is from tag cleavage

1   SERMETLYSALAPHEVALALAGLYTHRMET
2   ILELEUTHRALATHRGLYLEUVALALAILE
3   GLUASNILELYSALAGLYASPLYSVALILE
4   ALATHRASNPROGLUTHRPHEGLUVALALA
5   GLULYSTHRVALLEUGLUTHRTYRVALARG
6   GLUTHRTHRGLULEULEUHISLEUTHRILE
7   GLYGLYGLUVALILELYSTHRTHRPHEASP
8   HISPROPHETYRVALLYSASPVALGLYPHE
9   VALGLUALAGLYLYSLEUGLNVALGLYASP
10   LYSLEULEUASPSERARGGLYASNVALLEU
11   VALVALGLUGLULYSLYSLEUGLUILEALA
12   ASPLYSPROVALLYSVALTYRASNPHELYS
13   VALASPASPPHEHISTHRTYRHISVALGLY
14   ASPASNGLUVALLEUVALHISASN

Samples:

sample_1: CthBIL4, [U-99% 13C; U-99% 15N], 1.2 mM; potassium phosphate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
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 HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

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

CING, Geerten W. Vuister - Structure validation

CYANA v3, Guntert, Mumenthaler and Wuthrich - structure solution

VNMRJ, Varian - collection

CcpNMR, CCPN - chemical shift assignment

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 800 MHz

Related Database Links:

NCBI 23020817
PDB
DBJ GAE90859
GB ABN53254 EIC12360
REF WP_038291414

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts