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- PDB-4y27: E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a... -

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Basic information

Entry
Database: PDB / ID: 4y27
TitleE.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662
Components27-mer 23S Sarcin-Ricil Loop
KeywordsRNA / modification / ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.998 Å
AuthorsEnnifar, E. / Micura, R. / Fluer, S.
Funding support Switzerland, Austria, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_143388/1 Switzerland
Austrian Science FoundationP21641 Austria
Austrian Science FoundationI1040 Austria
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis.
Authors: Koch, M. / Flur, S. / Kreutz, C. / Ennifar, E. / Micura, R. / Polacek, N.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 2.0May 15, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_seq_map_depositor_info / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.pdbx_auth_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_PDB_residue_no / _chem_comp.mon_nstd_flag / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 27-mer 23S Sarcin-Ricil Loop


Theoretical massNumber of molelcules
Total (without water)8,7561
Polymers8,7561
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint1 kcal/mol
Surface area4810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.500, 29.500, 77.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain 27-mer 23S Sarcin-Ricil Loop


Mass: 8756.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.83 % / Description: Square platelet
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown for two weeks at 20C by mixing one volume of RNA sample with one volume of a crystallization buffer made with ammonium sulfate 2.5 M, magnesium acetate 10 mM and 2-(N- ...Details: Crystals were grown for two weeks at 20C by mixing one volume of RNA sample with one volume of a crystallization buffer made with ammonium sulfate 2.5 M, magnesium acetate 10 mM and 2-(N-morpholino)ethanesulfonic acid (MES) pH 5.6 50 mM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.77491 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77491 Å / Relative weight: 1
ReflectionResolution: 0.998→30 Å / Num. obs: 35632 / % possible obs: 99.8 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 35.15
Reflection shellResolution: 0.998→1.02 Å / Rmerge(I) obs: 3.697 / Mean I/σ(I) obs: 1.01 / Num. unique all: 2556 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 0.998→29.5 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1488 1770 4.97 %
Rwork0.1353 --
obs0.1361 35630 99.85 %
Solvent computationShrinkage radii: 0.3 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.998→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 0 143 723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016647
X-RAY DIFFRACTIONf_angle_d1.5791003
X-RAY DIFFRACTIONf_dihedral_angle_d11.91299
X-RAY DIFFRACTIONf_chiral_restr0.09132
X-RAY DIFFRACTIONf_plane_restr0.01927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9983-1.02530.32671290.31142567X-RAY DIFFRACTION98
1.0253-1.05540.26971350.24362605X-RAY DIFFRACTION100
1.0554-1.08950.22271380.20252591X-RAY DIFFRACTION100
1.0895-1.12840.21811290.17442612X-RAY DIFFRACTION100
1.1284-1.17360.16521390.15792585X-RAY DIFFRACTION100
1.1736-1.2270.15871410.14212628X-RAY DIFFRACTION100
1.227-1.29170.16141390.13522588X-RAY DIFFRACTION100
1.2917-1.37260.15231330.13452591X-RAY DIFFRACTION100
1.3726-1.47860.1421370.13342615X-RAY DIFFRACTION100
1.4786-1.62740.1431370.11962601X-RAY DIFFRACTION100
1.6274-1.86290.14621360.11632613X-RAY DIFFRACTION100
1.8629-2.34690.14731360.13582623X-RAY DIFFRACTION100
2.3469-29.51290.13131410.12542641X-RAY DIFFRACTION100

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