BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 11077

Title: Solution structure of the E. coli ribosome hibernation promoting factor HPF   PubMed: 19747895

Deposition date: 2009-08-13 Original release date: 2009-10-14

Authors: Sato, Akiko; Mishima, Masaki

Citation: Sato, Akiko; Watanabe, Takumi; Maki, Yasushi; Ueta, Masami; Yoshida, Hideji; Ito, Yutaka; Wada, Akira; Mishima, Masaki. "Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function."  Biochem. Biophys. Res. Commun. 389, 580-585 (2009).

Assembly members:
HPF, polymer, 95 residues, 10767.349 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pQE9

Entity Sequences (FASTA):
HPF: MQLNITGNNVEITEALREFV TAKFAKLEQYFDRINQVYVV LKVEKVTHTSDATLHVNGGE IHASAEGQDMYAAIDGLIDK LARQLTKHKDKLKQH

Data sets:
Data typeCount
13C chemical shifts312
15N chemical shifts94
1H chemical shifts641

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1HPF1

Entities:

Entity 1, HPF 95 residues - 10767.349 Da.

The residue Met-1 is derived from the expression vector. Native protein sequence starts second Gln as Gln-1.

1   METGLNLEUASNILETHRGLYASNASNVAL
2   GLUILETHRGLUALALEUARGGLUPHEVAL
3   THRALALYSPHEALALYSLEUGLUGLNTYR
4   PHEASPARGILEASNGLNVALTYRVALVAL
5   LEULYSVALGLULYSVALTHRHISTHRSER
6   ASPALATHRLEUHISVALASNGLYGLYGLU
7   ILEHISALASERALAGLUGLYGLNASPMET
8   TYRALAALAILEASPGLYLEUILEASPLYS
9   LEUALAARGGLNLEUTHRLYSHISLYSASP
10   LYSLEULYSGLNHIS

Samples:

sample_1: HPF, [U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; H2O 93%; D2O 7%

sample_2: HPF, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; H2O 93%; D2O 7%

sample_3: HPF, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; D2O 100%

sample_4: HPF, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; Pf1 phage 15 mg/mL; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.9; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D CBCANHsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HNCO No.1sample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
4D H(CCO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D HN(CO)HBsample_2isotropicsample_conditions_1
3D HNCO No.2sample_4anisotropicsample_conditions_1

Software:

NMRPipe v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

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

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

SPARKY v3.113, Goddard - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAA02316 BAB37505 BAE77247 BAG79011 BAI27481
EMBL CAA81618 CAP77663 CAQ33536 CAR00165 CAR04813
GB AAA58005 AAB60164 AAC76235 AAG58337 AAN44709
REF NP_312109 NP_417670 NP_709002 WP_001176593 WP_001176595
SP P0AFX0 P0AFX1 P0AFX2 P0AFX3
TPD FAA00071
AlphaFold P0AFX2 P0AFX1 P0AFX0 P0AFX3

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