BMRB Entry 19550

Name: Domain 1 of E. coli ribosomal protein S1
Published: 2014-04-14

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PDB ID: 2mfi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19550
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 1 of E. coli ribosomal protein S1

Deposition date:

2013-10-11

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:
S1F1, polymer, 96 residues, 10408.6085 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: pET151:D-TOPO

Entity Sequences (FASTA):

Entity Sequences (FASTA):
S1F1: GIDPFTESLKEIETRPGSIV RGVVVAIDKDVVLVDAGLKS ESAIPAEQFKNAQGELEIQV GDEVDVALDAVEDGFGETLL SREKAKRHEAWITLEK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	389
15N chemical shifts	95
1H chemical shifts	659

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	S1F1	1

Entities:

Entity 1, S1F1 96 residues - 10408.6085 Da.

The six first residues are generated by TOPO cloning and TEV cleavage.

1

GLY

ILE

ASP

PRO

PHE

THR

GLU

SER

LEU

LYS

2

GLU

ILE

GLU

THR

ARG

PRO

GLY

SER

ILE

VAL

3

ARG

GLY

VAL

ALA

ILE

ASP

LYS

ASP

4

VAL

LEU

VAL

ASP

ALA

GLY

LEU

LYS

SER

5

GLU

SER

ALA

ILE

PRO

ALA

GLU

GLN

PHE

LYS

6

ASN

ALA

GLN

GLY

GLU

LEU

GLU

ILE

GLN

VAL

7

GLY

ASP

GLU

VAL

ASP

VAL

ALA

LEU

ASP

ALA

8

VAL

GLU

ASP

GLY

PHE

GLY

GLU

THR

LEU

9

SER

ARG

GLU

LYS

ALA

LYS

ARG

HIS

GLU

ALA

10

TRP

ILE

THR

LEU

GLU

LYS

Samples:

S1F1-15N13C-H2O: S1F1, [U-99% 13C; U-99% 15N], 0.2 ± 2e-05 mM; potassium phosphate 25.0 ± 0.0025 mM; potassium chloride 200.0 ± 0.0025 mM; H2O 93%; D2O, [U-100% 2H], 7%

S1F1-15N13C-D2O: S1F1, [U-99% 13C; U-99% 15N], 0.2 ± 2e-05 mM; potassium phosphate 25.0 ± 0.0025 mM; potassium chloride 200.0 ± 0.0025 mM; D2O, [U-100% 2H], 100%

S1F1-15N: S1F1, [U-99% 13C; U-99% 15N], 0.5 ± 2e-05 mM; potassium phosphate 25.0 ± 0.0025 mM; potassium chloride 200.0 ± 0.0025 mM; H2O 93%; D2O, [U-100% 2H], 7%

Condition_1: ionic strength: 0.200 M; pH: 6.500; pressure: 1.000 atm; temperature: 293.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	S1F1-15N13C-H2O	isotropic	Condition_1
3D HNCA	S1F1-15N13C-H2O	isotropic	Condition_1
3D HN(CO)CA	S1F1-15N13C-H2O	isotropic	Condition_1
3D HNCACB	S1F1-15N13C-H2O	isotropic	Condition_1
3D HCCH-TOCSY	S1F1-15N13C-D2O	isotropic	Condition_1
3D HNCO	S1F1-15N13C-H2O	isotropic	Condition_1
3D HN(CA)CO	S1F1-15N13C-H2O	isotropic	Condition_1
3D 1H-15N NOESY	S1F1-15N	isotropic	Condition_1
3D 1H-13C NOESY	S1F1-15N13C-D2O	isotropic	Condition_1
2D 1H-13C HSQC	S1F1-15N13C-D2O	isotropic	Condition_1
3D CCH-TOCSY	S1F1-15N13C-D2O	isotropic	Condition_1
3D HCCH-TOCSY aromatic	S1F1-15N13C-D2O	isotropic	Condition_1
2D 1H-1H NOESY	S1F1-15N13C-D2O	isotropic	Condition_1

Software:

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

TOPSPIN v3.1, Bruker, Guntert, Mumenthaler and Wuthrich - 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

UniProt	P0AG67
BMRB	19554
PDB	2MFI 2MFL 4Q7J 4R71 4TOI
DBJ	BAA35655 BAB34417 BAG76494 BAH62634 BAI24353
EMBL	CAA23630 CAA23644 CAD05381 CAP75381 CAQ31439
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