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- PDB-1gqe: Polypeptide Chain Release Factor 2 (RF2) from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1gqe
TitlePolypeptide Chain Release Factor 2 (RF2) from Escherichia coli
ComponentsRELEASE FACTOR 2
KeywordsTRANSLATION / PROTEIN SYNTHESIS / RIBOSOME / MACROMOLECULAR MIMICRY
Function / homology
Function and homology information


translation release factor activity, codon specific / translational termination / viral translational frameshifting / cytosol
Similarity search - Function
Release factor / Alpha-Beta Plaits - #1660 / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I ...Release factor / Alpha-Beta Plaits - #1660 / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Double Stranded RNA Binding Domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peptide chain release factor RF2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.81 Å
AuthorsVestergaard, B. / Kjeldgaard, M.
CitationJournal: Mol.Cell / Year: 2001
Title: Bacterial Polypeptide Release Factor Rf2 is Structurally Distinct from Eukaryotic Erf1.
Authors: Vestergaard, B. / Van, L. / Andersen, G. / Nyborg, J. / Buckingham, R. / Kjeldgaard, M.
History
DepositionNov 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RELEASE FACTOR 2


Theoretical massNumber of molelcules
Total (without water)41,6791
Polymers41,6791
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.388, 49.893, 63.144
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RELEASE FACTOR 2 / RF2


Mass: 41678.660 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P07012
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION: THR(246)ALA. RESIDUE 298 CORRESPONDS TO A LEUCINE IN THE SWISS-PROT SEQUENCE, ...ENGINEERED MUTATION: THR(246)ALA. RESIDUE 298 CORRESPONDS TO A LEUCINE IN THE SWISS-PROT SEQUENCE, BUT IS CLEARLY IDENTIFIED AS A VALINE IN ELECTRON DENSITY.
Has protein modificationY
Sequence detailsCRYSTALS FROM MUTANT T246A. RESIDUE 298 CORRESPONDS TO A LEUCINE IN THE SWISS-PROT SEQUENCE, BUT IS ...CRYSTALS FROM MUTANT T246A. RESIDUE 298 CORRESPONDS TO A LEUCINE IN THE SWISS-PROT SEQUENCE, BUT IS CLEARLY IDENTIFIED AS A VALINE IN ELECTRON DENSITY.

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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: 2.154 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.6
Details: 40 MM TRISHCL, PH 7.6, 400 MM NACL, 40 MM MGCL2, 2% ETHYLENE GLYCOL 20 MM DTT, PEG 2K MME 28-34%
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMTris-HCl1reservoirpH7.6
2400 mM1reservoirNaCl
340 mM1reservoirMgCl2
42 %ethylene glycol1reservoir
520 mMdithiothreitol1reservoir
628-34 %PEG2000 MME1reservoir
73.5 mg/mlprotein1dropand 8.0mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 59537 / % possible obs: 95.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / % possible all: 85.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 58787 / % possible obs: 95.9 % / Num. measured all: 1018104 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 71.2 % / Rmerge(I) obs: 0.319

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.81→18.18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1828329.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT RESTRAINED BY SAD PHASES REGION 247 - 257 WAS NOT VISIBLE IN THE ELECTRON DENSITY, BUT WAS MODELLED STEREOCHEMICALLY ACCORDING TO STRUCTURAL SIMILARITY WITH THE GGR MOTIF IN ...Details: REFINEMENT RESTRAINED BY SAD PHASES REGION 247 - 257 WAS NOT VISIBLE IN THE ELECTRON DENSITY, BUT WAS MODELLED STEREOCHEMICALLY ACCORDING TO STRUCTURAL SIMILARITY WITH THE GGR MOTIF IN RIBOSOMAL PROTEIN S5 (1FJF) AND THE GGQ MOTIF IN ERF1 (1DT9)
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1517 5 %RANDOM
Rwork0.222 ---
obs0.222 30515 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2865 Å2 / ksol: 0.395009 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å23.64 Å2
2---3.52 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.81→18.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 0 286 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 243 5.6 %
Rwork0.278 4116 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 59537 / Num. reflection Rfree: 2957 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.687
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / Rfactor obs: 0.278

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