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Biological Magnetic Resonance Data Bank


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BMRB Entry 30456

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30456
MolProbity Validation Chart

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Title: Solution structure of Trigger Factor dimer   PubMed: 29714686

Deposition date: 2018-04-22 Original release date: 2018-06-07

Authors: Saio, T.; Kawagoe, S.; Ishimori, K.; Kalodimos, C.

Citation: Saio, T.; Kawagoe, S.; Ishimori, K.; Kalodimos, C.. "Oligomerization of a molecular chaperone modulates its activity."  Elife 7, e35731-e35731 (2018).

Assembly members:
entity_1, polymer, 443 residues, 49696.199 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 83334   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

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

Entity Sequences (FASTA):
entity_1: MNHKVHHHHHHMQVSVETTQ GLGRRVTITIAADSIETAVK SELVNVAKKVRIDGFRKGKV PMNIVAQRYGASVRQDVLGD LMSRNFIDAIIKEKINPAGA PTYVPGEYKLGEDFTYSVEF EVYPEVELQGLEAIEVEKPI VEVTDADVDGMLDTLRKQQA TWKEKDGAVEAEDRVTIDFT GSVDGEEFEGGKASDFVLAM GQGRMIPGFEDGIKGHKAGE EFTIDVTFPEEYHAENLKGK AAKFAINLKKVEERELPELT AEFIKRFGVEDGSVEGLRAE VRKNMERELKSAIRNRVKSQ AIEGLVKANDIDVPAALIDS EIDVLRRQAAQRFGGNEKQA LELPRELFEEQAKRRVVVGL LLGEVIRTNELKADEERVKG LIEEMASAYEDPKEVIEFYS KNKELMDNMRNVALEEQAVE AVLAKAKVTEKETTFNELMN QQA

Data sets:
Data typeCount
13C chemical shifts280
15N chemical shifts331
1H chemical shifts1059

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21

Entities:

Entity 1, entity_1, 1 443 residues - 49696.199 Da.

1   METASNHISLYSVALHISHISHISHISHIS
2   HISMETGLNVALSERVALGLUTHRTHRGLN
3   GLYLEUGLYARGARGVALTHRILETHRILE
4   ALAALAASPSERILEGLUTHRALAVALLYS
5   SERGLULEUVALASNVALALALYSLYSVAL
6   ARGILEASPGLYPHEARGLYSGLYLYSVAL
7   PROMETASNILEVALALAGLNARGTYRGLY
8   ALASERVALARGGLNASPVALLEUGLYASP
9   LEUMETSERARGASNPHEILEASPALAILE
10   ILELYSGLULYSILEASNPROALAGLYALA
11   PROTHRTYRVALPROGLYGLUTYRLYSLEU
12   GLYGLUASPPHETHRTYRSERVALGLUPHE
13   GLUVALTYRPROGLUVALGLULEUGLNGLY
14   LEUGLUALAILEGLUVALGLULYSPROILE
15   VALGLUVALTHRASPALAASPVALASPGLY
16   METLEUASPTHRLEUARGLYSGLNGLNALA
17   THRTRPLYSGLULYSASPGLYALAVALGLU
18   ALAGLUASPARGVALTHRILEASPPHETHR
19   GLYSERVALASPGLYGLUGLUPHEGLUGLY
20   GLYLYSALASERASPPHEVALLEUALAMET
21   GLYGLNGLYARGMETILEPROGLYPHEGLU
22   ASPGLYILELYSGLYHISLYSALAGLYGLU
23   GLUPHETHRILEASPVALTHRPHEPROGLU
24   GLUTYRHISALAGLUASNLEULYSGLYLYS
25   ALAALALYSPHEALAILEASNLEULYSLYS
26   VALGLUGLUARGGLULEUPROGLULEUTHR
27   ALAGLUPHEILELYSARGPHEGLYVALGLU
28   ASPGLYSERVALGLUGLYLEUARGALAGLU
29   VALARGLYSASNMETGLUARGGLULEULYS
30   SERALAILEARGASNARGVALLYSSERGLN
31   ALAILEGLUGLYLEUVALLYSALAASNASP
32   ILEASPVALPROALAALALEUILEASPSER
33   GLUILEASPVALLEUARGARGGLNALAALA
34   GLNARGPHEGLYGLYASNGLULYSGLNALA
35   LEUGLULEUPROARGGLULEUPHEGLUGLU
36   GLNALALYSARGARGVALVALVALGLYLEU
37   LEULEUGLYGLUVALILEARGTHRASNGLU
38   LEULYSALAASPGLUGLUARGVALLYSGLY
39   LEUILEGLUGLUMETALASERALATYRGLU
40   ASPPROLYSGLUVALILEGLUPHETYRSER
41   LYSASNLYSGLULEUMETASPASNMETARG
42   ASNVALALALEUGLUGLUGLNALAVALGLU
43   ALAVALLEUALALYSALALYSVALTHRGLU
44   LYSGLUTHRTHRPHEASNGLULEUMETASN
45   GLNGLNALA

Samples:

sample_1: TF, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 2.2 mM

sample_2: TF, [Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.6 mM; Trigger Factor, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3], 0.6 mM

sample_3: RBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.3 mM; PPD-SBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3], 0.3 mM

sample_4: RBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.3 mM

sample_5: PPD, [U-99% 13C; U-99% 15N], 0.8 mM

sample_6: SBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.5 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 295 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 308 K

sample_conditions_4: ionic strength: 100 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 295 K

Experiments:

NameSampleSample stateSample conditions
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_1isotropicsample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_1isotropicsample_conditions_2
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_1isotropicsample_conditions_3
3D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQCsample_2isotropicsample_conditions_4
13C-edited SOFAST-NOESY-HMQCsample_2isotropicsample_conditions_4
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_3isotropicsample_conditions_4
3D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQCsample_3isotropicsample_conditions_4
13C-edited SOFAST-NOESY-HMQCsample_3isotropicsample_conditions_4
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_6isotropicsample_conditions_1
3D (1H)-15N HMQC-NOESY-1H-13C HMQCsample_6isotropicsample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-15N HMQCsample_6isotropicsample_conditions_1
13C-edited NOESY-HMQCsample_6isotropicsample_conditions_4
15N-edited NOESY-HSQCsample_6isotropicsample_conditions_1
13C-edited NOESY-HSQCsample_5isotropicsample_conditions_1
15N-edited NOESY-HSQCsample_5isotropicsample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-13C HMQCsample_4isotropicsample_conditions_1
13C-edited NOESY-HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HMQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HMQCsample_1isotropicsample_conditions_2
2D 1H-13C HMQCsample_1isotropicsample_conditions_3
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_4

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

OLIVIA, Masashi Yokochi - chemical shift assignment

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

NMR spectrometers:

  • Bruker AvanceIII 800 MHz
  • Bruker AvanceIII 700 MHz
  • Bruker AvanceIII 600 MHz
  • Varian UNITY 800 MHz
  • Varian UNITY 600 MHz

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