Interaction information

Interaction summary

Short label: Ribosomal large subunit pseudouridine synthase F-stem loop fragment of E. Coli 23S RNA
Full name: Ribosomal large subunit pseudouridine synthase F interacts with stem loop fragment of E. Coli 23S RNA
Source database: RCSB PDB
ID: 3DH3
Date modified: 2011-03-25 11:02:23 JST

Protein information

Short label

Ribosomal large subunit pseudouridine synthase F

Full name

Chain A,B,C,D of model 3DH3: Ribosomal large subunit pseudouridine synthase F

Gene

rluF (23S rRNA U2604 pseudouridine synthase)

GeneID

948519

Official symbol

rluF

Synonyms

3 synonym(s)

ECK4014
JW3982
yjbC

Description

23S rRNA U2604 pseudouridine synthase

Origin

Escherichia coli

NCBI Taxonomy ID

562

Name

Escherichia coli

Synonyms

16 synonym(s).

"Bacillus coli" Migula 1895
"Bacterium coli commune" Escherich 1885
"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Escherichia coli (Migula 1895) Castellani and Chalmers 1919
Escherichia coli retron Ec107
Escherichia coli retron Ec67
Escherichia coli retron Ec79
Escherichia coli retron Ec86
Eschericia coli
bacterium 10a
bacterium E3

Cross references

1 item(s)

UniProt: P32684

Sequence

3DH3A:Ribosomal large subunit pseudouridine synthase F

RNA information

Short label: stem loop fragment of E. Coli 23S RNA
Full name: Chain E,F,G,H of model 3DH3: stem loop fragment of E. Coli 23S RNA
Sequence: 3DH3E:stem loop fragment of E. Coli 23S RNA

Experiments (1)

Experiment 1

alian-2009

Full name

X-ray diffraction

Detection method

x-ray crystallography (MI:0114)

Term ID

MI:0114

Name

x-ray crystallography

Definition

Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallisation conditions.

Synonyms

2 synonym(s)

X-ray (PSI-MI-alternate)
x-ray diffraction (PSI-MI-short)

Is-a

2 item(s)

MI:0013: biophysical
MI:0659: experimental feature detection

Host organisms

1 host organism(s)

Origin

Escherichia coli

NCBI Taxonomy ID

562

Name

Escherichia coli

Synonyms

16 synonym(s).

"Bacillus coli" Migula 1895
"Bacterium coli commune" Escherich 1885
"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Escherichia coli (Migula 1895) Castellani and Chalmers 1919
Escherichia coli retron Ec107
Escherichia coli retron Ec67
Escherichia coli retron Ec79
Escherichia coli retron Ec86
Eschericia coli
bacterium 10a
bacterium E3

Reference

ALIAN, Akram, et al., J. Mol. Biol. 2009 May;388(4):785-800

PMID

19298824

Title

Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.

Authors

ALIAN, Akram, et al.

ALIAN, Akram
DEGIOVANNI, Andrew
GRINER, Sarah L
FINER-MOORE, Janet S
STROUD, Robert M

Citation

J. Mol. Biol. 2009 May;388(4):785-800

References (1)

Reference 1

ALIAN, Akram, et al., J. Mol. Biol. 2009 May;388(4):785-800

PMID

19298824

Title

Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.

Authors

ALIAN, Akram, et al.

ALIAN, Akram
DEGIOVANNI, Andrew
GRINER, Sarah L
FINER-MOORE, Janet S
STROUD, Robert M

Citation

J. Mol. Biol. 2009 May;388(4):785-800

Attributes (3)

Attributes

3 attribute(s)

3d-structure: Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate
3d-resolution: 3.00A
3d-r-factors: working 23.123%, free 27.899%

Interaction information