BMRB Entry 11060

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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/BMR11060
MolProbity Validation Chart

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Title:
Unusual Thermal Disassembly of the SPFH Domain Oligomer from Pyrococcus horikoshii
Deposition date:
2008-11-26
Original release date:
2010-01-11
Authors:
Kuwahara, Yohta; Unzai, Satoru; Nagata, Takashi; Hiroaki, Yoko; Yokoyama, Hideshi; Matsui, Ikuo; Ikegami, Takahisa; Fujiyoshi, Yoshinori; Hiroaki, Hidekazu
Citation:

Citation: Kuwahara, Yohta; Unzai, Satoru; Nagata, Takashi; Hiroaki, Yoko; Yokoyama, Hideshi; Matsui, Ikuo; Ikegami, Takahisa; Fujiyoshi, Yoshinori; Hiroaki, Hidekazu. "Unusual Thermal Disassembly of the SPFH Domain Oligomer from Pyrococcus horikoshii"  Biophysical J. 97, 2034-2043 (2009).
PubMed: 19804735

Assembly members:

Assembly members:
SPFH domain, polymer, 113 residues, 12868.851 Da.

Natural source:

Natural source:   Common Name: Pyrococcus horikoshii   Taxonomy ID: 53953   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus horikoshii

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-4T3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SPFH domain: GSDHVDLREHVIDVPPQEVI CKDNVVVTVDAVVYYQVIDP VKAVYNVSDFLMAIVKLAQT NLRAIIGEMELDETLSGRDI INARLREELDKITDRWGVKI TRVEIQRIDPPKD

Data sets:
Data typeCount
13C chemical shifts395
15N chemical shifts115
1H chemical shifts807

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SPFH domain1

Entities:

Entity 1, SPFH domain 113 residues - 12868.851 Da.

Residues 62-65 represent cloning artifacts

1   GLYSERASPHISVALASPLEUARGGLUHIS
2   VALILEASPVALPROPROGLNGLUVALILE
3   CYSLYSASPASNVALVALVALTHRVALASP
4   ALAVALVALTYRTYRGLNVALILEASPPRO
5   VALLYSALAVALTYRASNVALSERASPPHE
6   LEUMETALAILEVALLYSLEUALAGLNTHR
7   ASNLEUARGALAILEILEGLYGLUMETGLU
8   LEUASPGLUTHRLEUSERGLYARGASPILE
9   ILEASNALAARGLEUARGGLUGLULEUASP
10   LYSILETHRASPARGTRPGLYVALLYSILE
11   THRARGVALGLUILEGLNARGILEASPPRO
12   PROLYSASP

Samples:

sample_1: SPFH domain, [U-100% 13C; U-100% 15N], 0.7 mM; HEPES 20 mM; H2O 90%; D2O 10%

sample_2: SPFH domain, [U-100% 13C], 0.8 mM; HEPES 20 mM; D2O 100%

sample_conditions_1: ionic strength: 0 mM; pH: 7.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CC(CO)NHsample_1isotropicsample_conditions_1
3D HCC(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 13C-editted NOESYsample_2isotropicsample_conditions_1
3D 15N-editted NOESYsample_1isotropicsample_conditions_1

Software:

CYANA v2.0.17, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis, refinement

SPARKY v3.106, Goddard - chemical shift assignment, refinement

xwinnmr v3.5, Bruker Biospin - collection

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 800 MHz
  • Varian INOVA 900 MHz

Related Database Links:

PDB
DBJ BAA29558
EMBL CAB50468
GB AEC52040
REF WP_013748594 WP_048053138 WP_048147080
TPE CCE71018

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