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- PDB-7l3r: 23S Sarcin Ricin Loop with a 3-deazapurine A2670 -

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Basic information

Entry
Database: PDB / ID: 7l3r
Title23S Sarcin Ricin Loop with a 3-deazapurine A2670
ComponentsRNA (27-MER)
KeywordsRNA / RNA modification / Ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsEnnifar, E. / Renard, E.
Funding support Austria, 5items
OrganizationGrant numberCountry
Austrian Science FundP31691 Austria
Austrian Science FundF8011-B Austria
Austrian Science FundP30370 Austria
Austrian Science Fund32773 Austria
Austrian Research Promotion Agency858017 Austria
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Impact of 3-deazapurine nucleobases on RNA properties.
Authors: Bereiter, R. / Himmelstoss, M. / Renard, E. / Mairhofer, E. / Egger, M. / Breuker, K. / Kreutz, C. / Ennifar, E. / Micura, R.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8352
Polymers8,7431
Non-polymers921
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.537, 29.537, 76.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: RNA chain RNA (27-MER)


Mass: 8743.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3-deaza A2670-modified SRL RNA / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.82656124355451 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656124355451 Å / Relative weight: 1
ReflectionResolution: 1.01→50 Å / Num. obs: 66875 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.07
Reflection shellResolution: 1.01→1.08 Å / Num. unique obs: 72259 / CC1/2: 0.809

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 1.01→20.14 Å / SU ML: 0.1431 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.4918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1389 3333 5 %
Rwork0.1245 63353 -
obs0.1252 66686 99.9 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.16 Å2
Refinement stepCycle: LAST / Resolution: 1.01→20.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 491 94 151 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089742
X-RAY DIFFRACTIONf_angle_d1.29761154
X-RAY DIFFRACTIONf_chiral_restr0.0559152
X-RAY DIFFRACTIONf_plane_restr0.019831
X-RAY DIFFRACTIONf_dihedral_angle_d11.6196361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.030.39391360.36822574X-RAY DIFFRACTION99.09
1.03-1.040.35511390.3072671X-RAY DIFFRACTION99.96
1.04-1.060.26721390.27872663X-RAY DIFFRACTION100
1.06-1.080.24781390.23362616X-RAY DIFFRACTION99.96
1.08-1.10.22571420.22232722X-RAY DIFFRACTION99.97
1.1-1.120.20951350.18482549X-RAY DIFFRACTION99.89
1.12-1.140.21161420.17462710X-RAY DIFFRACTION99.82
1.14-1.160.16621350.15272614X-RAY DIFFRACTION100
1.16-1.190.17491380.14312635X-RAY DIFFRACTION100
1.19-1.210.15081400.12922644X-RAY DIFFRACTION100
1.21-1.240.12851380.12882642X-RAY DIFFRACTION99.93
1.24-1.280.12931420.12052650X-RAY DIFFRACTION99.93
1.28-1.320.1541360.12132617X-RAY DIFFRACTION99.96
1.32-1.360.16621410.12062656X-RAY DIFFRACTION100
1.36-1.410.16151390.12222671X-RAY DIFFRACTION100
1.41-1.460.14951360.1192590X-RAY DIFFRACTION99.93
1.46-1.530.18181410.1132671X-RAY DIFFRACTION100
1.53-1.610.11231370.10092650X-RAY DIFFRACTION99.96
1.61-1.710.12331420.09392643X-RAY DIFFRACTION100
1.71-1.840.13651400.09752640X-RAY DIFFRACTION100
1.84-2.030.1471360.11532607X-RAY DIFFRACTION100
2.03-2.320.14071410.12722653X-RAY DIFFRACTION100
2.32-2.920.14761410.13212647X-RAY DIFFRACTION99.75
2.93-20.140.10321380.1152618X-RAY DIFFRACTION99.39

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