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- PDB-1c2x: 5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.... -

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Entry
Database: PDB / ID: 1c2x
Title5S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION
Descriptor5S RIBOSOMAL RNA
KeywordsRIBOSOME / 5S RRNA / 23S RRNA / LARGE RIBOSOMAL SUBUNIT / PROTEIN BIOSYNTHESIS / RIBONUCLEIC ACID / EM-RECONSTRUCTION / ATOMIC STRUCTURE / 3D ARRANGEMENT / FITTING
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.5 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsBrimacombe, R. / Mueller, F.
CitationJ. Mol. Biol., 2000, 298, 35-59

primary. J. Mol. Biol., 2000, 298, 35-59 StrPapers
The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
F Mueller / I Sommer / P Baranov / R Matadeen / M Stoldt / J Wöhnert / M Görlach / M van Heel / R Brimacombe

#1. J.Mol.Biol., 1997, 271, 524-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. I. Fitting the RNA to a 3D Electron Microscopic Map at 20 Angstroms
Mueller, F. / Brimacombe, R.

#2. J.Mol.Biol., 1997, 271, 545-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. II. The RNA-Protein Interaction Data
Mueller, F. / Brimacombe, R.

#3. J.Mol.Biol., 1997, 271, 566-
A New Model for the Three-Dimensional Folding of Escherichia Coli 16S Ribosomal RNA. III. The Topography of the Functional Centre
Mueller, F. / Stark, H. / Van Heel, M. / Rinke-Appel, J. / Brimacombe, R.

DateDeposition: Jul 28, 1999 / Release: Apr 10, 2000 / Last modification: Feb 24, 2009

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Assembly

Deposited unit
C: 5S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)38,7901
Polyers38,7901
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain5S RIBOSOMAL RNA / 5S RRNA


Mass: 38790.309 Da / Num. of mol.: 1 / Details: THIRD OF THE 3 RRNA CHAINS OF THE RIBOSOME
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenAggregation state: PARTICLE
CrystalDescription: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

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Processing

SoftwareName: ERNA-3D / Classification: refinement
ComputingStructure refinement: ERNA-3D
EM single particle entitySymmetry type: ASYMMETRIC
Atomic model buildingDetails: THIS FILE HAS BEEN GENERATED BY THE USE OF ALL RELEVANT BIOCHEMICAL CONSTRAINTS AND THE CONSTRAINTS GIVEN BY THE ELECTRON DENSITY CONTOUR OF THE RIBOSOME, WHICH WAS DERIVED FROM THE CRYO-ELECTRON MICROSCOPIC RECONSTRUCTION. THIS FILE IS PART OF A SET OF ALL THREE RIBONUCLEIC ACID CHAINS OF THE RIBOSOME TOGETHER WITH A NUMBER OF RIBOSOMAL PROTEINS WHICH ARE ALSO DEPOSITED WITH THE PDB DATA BANK. THE ATOMIC COORDINATES OF ALL THESE RIBOSOMAL COMPONENTS REFLECT THEIR POSITIONS IN THE 70S RIBOSOME.
Ref space: REAL
Atomic model building
PDB-ID 3D fitting idID
1C2X11
1C2X12
Least-squares processHighest resolution: 7.5 A
Refine hist #LASTHighest resolution: 7.5 A
Number of atoms included #LASTProtein: 0 / Nucleic acid: 2570 / Ligand: 0 / Solvent: 0 / Total: 2570

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