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- PDB-1ek8: CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESC... -

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Basic information

Entry
Database: PDB / ID: 1ek8
TitleCRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI
ComponentsRIBOSOME RECYCLING FACTOR
KeywordsTRANSLATION / ribosome / translation factor / t-RNA mimicry / coiled coil
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / translation / cytoplasm / 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
DECYLOXY-METHANOL / : / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMin, K. / Suh, S.W. / Kim, K.K.
Citation
Journal: EMBO J. / Year: 2000
Title: Crystal structure of the ribosome recycling factor from Escherichia coli.
Authors: Kim, K.K. / Min, K. / Suh, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Studies of Ribosome Recycling Factor from Escherichia coli.
Authors: Yun, J. / Kim, W. / Ha, S.C. / Eom, S.H. / Suh, S.W. / Kim, K.K.
History
DepositionMar 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOME RECYCLING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4625
Polymers20,6721
Non-polymers7904
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.064, 48.064, 142.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RIBOSOME RECYCLING FACTOR / RIBOSOME RELEASING FACTOR / RRF


Mass: 20671.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P0A805
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-DEM / DECYLOXY-METHANOL


Mass: 188.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES-NaOH, 10 % PEG 350 MME, 12 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal
*PLUS
Density % sol: 53.4 %
Crystal grow
*PLUS
Temperature: 14 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMES-NaOH1reservoir
210 %PEG350 MME1reservoir
312-14 %PEG4001reservoir
41.8 mMdecyl-beta-D-maltopyranoside1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0074
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0074 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 29485 / Num. obs: 8691 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.23 / Num. unique all: 858 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 29485
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. unique obs: 858 / Rmerge(I) obs: 0.23

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 885 -random
Rwork0.228 ---
all0.237 9017 --
obs0.235 8391 93.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 16 230 1683
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.010377
X-RAY DIFFRACTIONc_bond_d1.63437
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.9 Å2

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