BMRB Entry 11077

Name: Solution structure of the E. coli ribosome hibernation promoting factor HPF
Published: 2009-10-14

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PDB ID: 2rql
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11077
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the E. coli ribosome hibernation promoting factor HPF

Deposition date:

2009-08-13

Original release date:

2009-10-14

Authors:

Sato, Akiko; Mishima, Masaki

Citation:

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).
PubMed: 19747895

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	312
15N chemical shifts	94
1H chemical shifts	641

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HPF	1

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

MET

GLN

LEU

ASN

ILE

THR

GLY

ASN

VAL

2

GLU

ILE

THR

GLU

ALA

LEU

ARG

GLU

PHE

VAL

3

THR

ALA

LYS

PHE

ALA

LYS

LEU

GLU

GLN

TYR

4

PHE

ASP

ARG

ILE

ASN

GLN

VAL

TYR

VAL

5

LEU

LYS

VAL

GLU

LYS

VAL

THR

HIS

THR

SER

6

ASP

ALA

THR

LEU

HIS

VAL

ASN

GLY

GLU

7

ILE

HIS

ALA

SER

ALA

GLU

GLY

GLN

ASP

MET

8

TYR

ALA

ILE

ASP

GLY

LEU

ILE

ASP

LYS

9

LEU

ALA

ARG

GLN

LEU

THR

LYS

HIS

LYS

ASP

10

LYS

LEU

LYS

GLN

HIS

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D CBCANH	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D HNCO No.1	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
4D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HN(CO)HB	sample_2	isotropic	sample_conditions_1
3D HNCO No.2	sample_4	anisotropic	sample_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

PDB	2RQL 3V26 3V28
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	P0AFX0 P0AFX1 P0AFX2 P0AFX3