BMRB Entry 19554

Name: Domain 2 of E. coli ribosomal protein S1
Published: 2014-04-14

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PDB ID: 2mfl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19554
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Domain 2 of E. coli ribosomal protein S1

Deposition date:

2013-10-12

Original release date:

2014-04-14

Authors:

GIRAUD, Pierre; CRECHET, Jean-Bernard; BONTEMS, Francois; UZAN, Marc; SIZUN, Christina

Citation:

Citation: Giraud, Pierre; Crechet, Jean-Bernard; Uzan, Marc; Bontems, Francois; Sizun, Christina. "Resonance assignment of the ribosome binding domain of E. coli ribosomal protein S1." Biomol. NMR Assignments ., .-. (2014).
PubMed: 24682851

Assembly members:

Assembly members:
S1F12, polymer, 182 residues, 10462.053 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
S1F12: GSHMTESFAQLFEESLKEIE TRPGSIVRGVVVAIDKDVVL VDAGLKSESAIPAEQFKNAQ GELEIQVGDEVDVALDAVED GFGETLLSREKAKRHEAWIT LEKAYEDAETVTGVINGKVK GGFTVELNGIRAFLPGSLVD VRPVRDTLHLEGKELEFKVI KLDQKRNNVVVSRRAVIESE NS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	668
15N chemical shifts	174
1H chemical shifts	1088

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	S1F12	1

Entities:

Entity 1, S1F12 182 residues - 10462.053 Da.

This sequence contains the two first domains of S1 separated by a flexible linker and an extended flexible N-terminal region

1

GLY

SER

HIS

MET

THR

GLU

SER

PHE

ALA

GLN

2

LEU

PHE

GLU

SER

LEU

LYS

GLU

ILE

GLU

3

THR

ARG

PRO

GLY

SER

ILE

VAL

ARG

GLY

VAL

4

VAL

ALA

ILE

ASP

LYS

ASP

VAL

LEU

5

VAL

ASP

ALA

GLY

LEU

LYS

SER

GLU

SER

ALA

6

ILE

PRO

ALA

GLU

GLN

PHE

LYS

ASN

ALA

GLN

7

GLY

GLU

LEU

GLU

ILE

GLN

VAL

GLY

ASP

GLU

8

VAL

ASP

VAL

ALA

LEU

ASP

ALA

VAL

GLU

ASP

9

GLY

PHE

GLY

GLU

THR

LEU

SER

ARG

GLU

10

LYS

ALA

LYS

ARG

HIS

GLU

ALA

TRP

ILE

THR

11

LEU

GLU

LYS

ALA

TYR

GLU

ASP

ALA

GLU

THR

12

VAL

THR

GLY

VAL

ILE

ASN

GLY

LYS

VAL

LYS

13

GLY

PHE

THR

VAL

GLU

LEU

ASN

GLY

ILE

14

ARG

ALA

PHE

LEU

PRO

GLY

SER

LEU

VAL

ASP

15

VAL

ARG

PRO

VAL

ARG

ASP

THR

LEU

HIS

LEU

16

GLU

GLY

LYS

GLU

LEU

GLU

PHE

LYS

VAL

ILE

17

LYS

LEU

ASP

GLN

LYS

ARG

ASN

VAL

18

VAL

SER

ARG

ALA

VAL

ILE

GLU

SER

GLU

19

ASN

SER

Samples:

S1F12-15N13C2H: S1F12, [U-99% 13C; U-99% 15N; U-80% 2H], 0.25 ± 0.025 mM; sodium phosphate 25.0 ± 1.0 mM; sodium chloride 200.0 ± 2.0 mM; H2O 93%; D2O, [U-100% 2H], 7%

S1F12-15N13C-H2O: S1F12, [U-99% 13C; U-99% 15N], 0.2 ± 0.02 mM; potassium phosphate 50.0 ± 1.0 mM; potassium chloride 200.0 ± 2.0 mM; H2O 93%; D2O, [U-100% 2H], 7%

S1F12-15N13C-D2O: S1F12, [U-99% 13C; U-99% 15N], 0.2 ± 0.02 mM; potassium phosphate 50.0 ± 1.0 mM; potassium chloride 200.0 ± 2.0 mM; D2O, [U-100% 2H], 100%

Condition_1: ionic strength: 0.200 M; pH: 6.800; pressure: 1.000 atm; temperature: 293.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	S1F12-15N13C2H	isotropic	Condition_1
3D HNCA	S1F12-15N13C2H	isotropic	Condition_1
3D HN(CO)CA	S1F12-15N13C2H	isotropic	Condition_1
3D HNCACB	S1F12-15N13C2H	isotropic	Condition_1
3D CBCA(CO)NH	S1F12-15N13C2H	isotropic	Condition_1
3D HNCO	S1F12-15N13C2H	isotropic	Condition_1
3D HN(CA)CO	S1F12-15N13C2H	isotropic	Condition_1
2D 1H-15N HSQC	S1F12-15N13C-H2O	isotropic	Condition_1
3D HBHA(CO)NH	S1F12-15N13C-H2O	isotropic	Condition_1
3D 1H-15N NOESY	S1F12-15N13C-H2O	isotropic	Condition_1
2D 1H-13C HSQC	S1F12-15N13C-D2O	isotropic	Condition_1
3D HCCH-TOCSY	S1F12-15N13C-D2O	isotropic	Condition_1
3D HCCH-TOCSY aromatic	S1F12-15N13C-D2O	isotropic	Condition_1
3D CCH-TOCSY	S1F12-15N13C-D2O	isotropic	Condition_1
2D 1H-1H TOCSY	S1F12-15N13C-D2O	isotropic	Condition_1
2D 1H-1H NOESY	S1F12-15N13C-D2O	isotropic	Condition_1
3D 1H-13C NOESY	S1F12-15N13C-D2O	isotropic	Condition_1

Software:

CCPNmr ANALYSIS v2.2, CCPN - Spectrum analysis, Spectrum display

TOPSPIN v3.1, Bruker, Herrmann, G?ntert and W?thrich - Spectrum processing, Structure calculation

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

TALOS+ vany, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Dihedral angles

NMR spectrometers:

Bruker Avance 950 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz

UNP	P0AG67
BMRB	19550
PDB	2MFI 2MFL 4Q7J 4R71
DBJ	BAA35655 BAB34417 BAG76494 BAH62634 BAI24353
EMBL	CAA23630 CAA23644 CAD05381 CAO97188 CAP75381
GB	AAC73997 AAG55396 AAL19915 AAN42537 AAN79519
PIR	AC0614
PRF	0804233A
REF	NP_309021 NP_415431 NP_455468 NP_459956 NP_706830
SP	P0AG67 P0AG68 P0AG69 P0AG70
AlphaFold	P77352 P0AG67 P0AG68 P0AG69 P0AG70