BMRB Entry 10138

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PDB ID: 2dog
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10138
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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:

Solution structure of the N-terminal domain of RimM from Thermus thermophilus HB8

Deposition date:

2007-06-04

Original release date:

2008-06-12

Authors:

Suzuki, S.; Matsumoto, E.; Tatsuguchi, A.; Kawazoe, M.; Kaminishi, T.; Takemoto, C.; Shirouzu, M.; Muto, Y.; Yokoyama, S.

Citation:

Citation: Suzuki, S.; Tatsuguchi, A.; Matsumoto, E.; Kawazoe, M.; Kaminishi, T.; Shirouzu, M.; Muto, Y.; Takemoto, C.; Yokoyama, S.. "Structural characterization of the ribosome maturation protein, RimM" J. Bacteriol. 189, .-6397 (6406).
PubMed: 17616598

Assembly members:

Assembly members:
RIEF fold, polymer, 85 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Thermus thermophilus Taxonomy ID: 300852 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermus thermophilus

Experimental source:

Experimental source: Production method: cell free synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RIEF fold: MRLVEIGRFGAPYALKGGLR FRGEPVVLHLERVYVEGHGW RAIEDLYRVGEELVVHLAGV TDRTLAEALVGLRVYAEVAD LPPLE

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	388
15N chemical shifts	82
1H chemical shifts	623

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Probable 16S rRNA-processing protein rimM	1

Entities:

Entity 1, Probable 16S rRNA-processing protein rimM 85 residues - Formula weight is not available

1

MET

ARG

LEU

VAL

GLU

ILE

GLY

ARG

PHE

GLY

2

ALA

PRO

TYR

ALA

LEU

LYS

GLY

LEU

ARG

3

PHE

ARG

GLY

GLU

PRO

VAL

LEU

HIS

LEU

4

GLU

ARG

VAL

TYR

VAL

GLU

GLY

HIS

GLY

TRP

5

ARG

ALA

ILE

GLU

ASP

LEU

TYR

ARG

VAL

GLY

6

GLU

LEU

VAL

HIS

LEU

ALA

GLY

VAL

7

THR

ASP

ARG

THR

LEU

ALA

GLU

ALA

LEU

VAL

8

GLY

LEU

ARG

VAL

TYR

ALA

GLU

VAL

ALA

ASP

9

LEU

PRO

LEU

GLU

Samples:

sample_1: RIEF fold, [U-13C; U-15N], 1.2 mM; sodium phosphate 20 mM; D2O 10%; H2O 90%

condition_1: ionic strength: 120 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	not available	condition_1
3D 13C-separated NOESY	sample_1	not available	condition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20031121, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.9321, Kobayashi, N. - data analysis

Olivia v1.10.5, Yokochi, M. - data analysis

CYANA v2.0.17, Guntert, P. - refinement, structure solution

SPARKY v3.110, Goddard, T.D., Kneller, D.G. - data analysis

NMR spectrometers:

Bruker AVANCE 800 MHz

BMRB	10139 10140
PDB	2DOG 2DYI 3A1P
DBJ	BAD70856
GB	AAS81019 AEG33454 AFH38925 EIA39096
REF	WP_008632437 WP_011228392 YP_144299
SP	Q5SJH5 Q72JU7
AlphaFold	Q5SJH5 Q72JU7