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- PDB-2b3t: Structure of complex between E. coli translation termination fact... -

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Basic information

Entry
Database: PDB / ID: 2b3t
TitleStructure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase
Components
  • Peptide chain release factor 1
  • Protein methyltransferase hemK
KeywordsTRANSLATION / release factor / translation termination / methylation / conformational changes
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / protein methyltransferase activity / protein methylation / translation release factor activity, codon specific / S-adenosylmethionine-dependent methyltransferase activity / translational termination / ribosome binding ...peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / protein methyltransferase activity / protein methylation / translation release factor activity, codon specific / S-adenosylmethionine-dependent methyltransferase activity / translational termination / ribosome binding / regulation of gene expression / nucleic acid binding / cytosol
Similarity search - Function
Helix Hairpins - #1980 / Alpha-Beta Plaits - #1660 / Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / : / PrmC N-terminal domain / Peptide chain release factor 1 / Methyltransferase small domain / Methyltransferase small domain ...Helix Hairpins - #1980 / Alpha-Beta Plaits - #1660 / Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / : / PrmC N-terminal domain / Peptide chain release factor 1 / Methyltransferase small domain / Methyltransferase small domain / : / Methyltransferase domain / Methyltransferase domain / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Ubiquitin-associated (UBA) domain / DNA methylase, N-6 adenine-specific, conserved site / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Helix Hairpins / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / Helix non-globular / Special / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Peptide chain release factor RF1 / Release factor glutamine methyltransferase / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGraille, M. / Heurgue-Hamard, V. / Champ, S. / Mora, L. / Scrima, N. / Ulryck, N. / van Tilbeurgh, H. / Buckingham, R.H.
CitationJournal: Mol.Cell / Year: 2005
Title: Molecular basis for bacterial class I release factor methylation by PrmC
Authors: Graille, M. / Heurgue-Hamard, V. / Champ, S. / Mora, L. / Scrima, N. / Ulryck, N. / van Tilbeurgh, H. / Buckingham, R.H.
History
DepositionSep 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Protein methyltransferase hemK
B: Peptide chain release factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8213
Polymers71,4372
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-2 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.540, 77.470, 89.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe heterodimer present in the asymetric unit corresponds to the biological unit.

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Components

#1: Protein Protein methyltransferase hemK / E.C.2.1.1.- / Protein-glutamine N- methyltransferase hemK / Protein-(glutamine-N5) MTase hemK / M.EcoKHemKP


Mass: 30877.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hemK / Production host: Escherichia coli (E. coli)
References: UniProt: P37186, UniProt: P0ACC1*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Peptide chain release factor 1 / RF-1


Mass: 40559.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfA, sueB, uar / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7I0
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: ammonium sulfate, NaCl, glycerol, Na Hepes, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 12.25 / Number: 52659 / Rmerge(I) obs: 10.4 / D res high: 3.1 Å / Num. obs: 14361 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
102046489.214
610162897.515.5
56149097.617.5
4533119818.6
3.54327597.4115.5
3.43.590296125.5
3.33.499195.5128.9
3.23.3107194.1140
3.13.2122991.8147.4
ReflectionResolution: 3.1→20 Å / Num. obs: 14670 / % possible obs: 96.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.25
Reflection shellResolution: 3.1→3.2 Å / % possible obs: 91.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.82 / Num. measured obs: 4594 / Num. unique obs: 1229

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
MOLREPphasing
CNSrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 732 4.9 %1T43 and 1GQE
Rwork0.244 ---
obs-14670 99.1 %-
Solvent computationBsol: 29.444 Å2
Displacement parametersBiso mean: 55.406 Å2
Baniso -1Baniso -2Baniso -3
1-5.413 Å20 Å20 Å2
2--9.779 Å20 Å2
3----15.191 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 26 0 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.3211.5
X-RAY DIFFRACTIONc_mcangle_it2.3582
X-RAY DIFFRACTIONc_scbond_it1.5952
X-RAY DIFFRACTIONc_scangle_it2.6362.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2sah.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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