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- PDB-1is1: Crystal structure of ribosome recycling factor from Vibrio paraha... -

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Basic information

Entry
Database: PDB / ID: 1is1
TitleCrystal structure of ribosome recycling factor from Vibrio parahaemolyticus
ComponentsRIBOSOME RECYCLING FACTOR
KeywordsTRANSLATION
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / cytosol
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 speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNakano, H. / Yamaichi, Y. / Uchiyama, S. / Yoshida, T. / Nishina, K. / Kato, H. / Ohkubo, T. / Honda, T. / Yamagata, Y. / Kobayashi, Y.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium
Authors: Nakano, H. / Yoshida, T. / Uchiyama, S. / Kawachi, M. / Matsuo, H. / Kato, T. / Ohshima, A. / Yamaichi, Y. / Honda, T. / Kato, H. / Yamagata, Y. / Ohkubo, T. / Kobayashi, Y.
History
DepositionNov 5, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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)20,6361
Polymers20,6361
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.799, 84.799, 142.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-252-

HOH

21A-299-

HOH

31A-314-

HOH

41A-352-

HOH

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Components

#1: Protein RIBOSOME RECYCLING FACTOR


Mass: 20635.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GRF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, sodium acetate, GDP, fusidic acid, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMMES/NaOH1reservoirpH6.2
3200 mMsodium acetate1reservoir
423-25 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 10326 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.2→2.24 Å / % possible all: 93.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 82069
Reflection shell
*PLUS
Rmerge(I) obs: 0.251

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 526 5.58 %RANDAM
Rwork0.203 ---
all-10271 --
obs-9422 --
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 227 1668
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection obs: 9947 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.005
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.078
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.207

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