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- PDB-1eh1: RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1eh1
TitleRIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS
ComponentsRIBOSOME RECYCLING FACTOR
KeywordsRIBOSOME / TRANSLATION / HINGE VARIABILITY
Function / homology
Function and homology information


ribosomal large subunit binding / translational termination / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle ...Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome-recycling factor
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.6 Å
AuthorsToyoda, T. / Tin, O.F. / Ito, K. / Fujiwara, T. / Kumasaka, T. / Yamamoto, M. / Garber, M.B. / Nakamura, Y.
CitationJournal: RNA / Year: 2000
Title: Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.
Authors: Toyoda, T. / Tin, O.F. / Ito, K. / Fujiwara, T. / Kumasaka, T. / Yamamoto, M. / Garber, M.B. / Nakamura, Y.
History
DepositionFeb 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOME RECYCLING FACTOR


Theoretical massNumber of molelcules
Total (without water)21,0291
Polymers21,0291
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.500, 71.50, 79.6
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBOSOME RECYCLING FACTOR


Mass: 21029.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WX76
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: ammonium sulphate, sodium acetate, MES, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
30.1 Msodium acetate trihydrate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 30, 1999 / Details: GRAPHITE CRYSTAL
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7568 / Num. obs: 28513 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.6
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.234 / Num. unique all: 7568 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 7568 / Num. measured all: 28513
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→10 Å / Data cutoff low absF: 0 / σ(F): 2 / σ(I): 3
Stereochemistry target values: RAMACHANDRAN ET AL BBA 359:298 (1974)
RfactorNum. reflection% reflectionSelection details
Rfree0.307 393 5.42 %RANDOM
Rwork0.234 ---
all0.268 7549 --
obs0.236 7394 99.7 %-
Displacement parametersBiso mean: 58.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 88 1566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3148 32 3.76 %
Rwork0.2755 820 -
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5.42 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.1

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