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- PDB-1y69: RRF domain I in complex with the 50S ribosomal subunit from Deino... -

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Basic information

Entry
Database: PDB / ID: 1y69
TitleRRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L16
  • 50S ribosomal protein L27
  • 5S ribosomal RNA
  • Ribosome-recycling factor
KeywordsRIBOSOME / 50S / RRF / RECYCLING FACTOR
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / cytosol / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L16/L10 / Aldehyde Oxidoreductase; domain 3 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Topoisomerase I; Chain A, domain 4 / Ribosomal protein L16 signature 1. ...Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L16/L10 / Aldehyde Oxidoreductase; domain 3 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Topoisomerase I; Chain A, domain 4 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L16 / Ribosomal protein L27 / Ribosomal L27 protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Alpha-Beta Complex / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome-recycling factor / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Deinococcus radiodurans R1 (radioresistant)
Deinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.33 Å
AuthorsWilson, D.N. / Schluenzen, F. / Harms, J.M. / Yoshida, T. / Ohkubo, T. / Albrecht, R. / Buerger, J. / Kobayashi, Y. / Fucini, P.
CitationJournal: EMBO J. / Year: 2005
Title: X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit
Authors: Wilson, D.N. / Schluenzen, F. / Harms, J.M. / Yoshida, T. / Ohkubo, T. / Albrecht, R. / Buerger, J. / Kobayashi, Y. / Fucini, P.
History
DepositionDec 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.src_method / _entity_name_com.name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id
Revision 1.4Aug 2, 2017Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Domain II of RRF (residues 31-105) was replaced by GLY-GLY-GLY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S ribosomal RNA
9: 5S ribosomal RNA
K: 50S ribosomal protein L16
U: 50S ribosomal protein L27
8: Ribosome-recycling factor


Theoretical massNumber of molelcules
Total (without water)1,011,8975
Polymers1,011,8975
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.700, 405.000, 693.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain 23S ribosomal RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: 1026245073
#2: RNA chain 5S ribosomal RNA


Mass: 39911.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: 11612676
#3: Protein 50S ribosomal protein L16


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ5
#4: Protein 50S ribosomal protein L27


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RY65
#5: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 12844.616 Da / Num. of mol.: 1 / Fragment: UNP residues 1-30 and 106-185 / Mutation: RRF domain II deletion and GGG insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: frr, rrf, b0172, JW0167 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A805

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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: 4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5HEPES11
6NH4CL11
7H2O11
8MGCL212
9KCL12
10NH4CL12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 343272 / Num. obs: 343272 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.8
Reflection shellResolution: 3.3→3.36 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.398 / % possible all: 86.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.33→8.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 117914.76 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.338 11832 5 %RANDOM
Rwork0.275 ---
all0.291 343272 --
obs0.275 238082 74.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.3143 Å2 / ksol: 0.118211 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--20.39 Å20 Å20 Å2
2--48.11 Å20 Å2
3----27.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.53 Å
Luzzati d res low-8 Å
Luzzati sigma a0.85 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3.33→8.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 61875 0 0 64484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.33→3.45 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.469 1309 5.2 %
Rwork0.456 24038 -
obs--75.7 %

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