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- PDB-4p8z: Speciation of a group I intron into a lariat capping ribozyme -

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Basic information

Entry
Database: PDB / ID: 4p8z
TitleSpeciation of a group I intron into a lariat capping ribozyme
ComponentsDidymium iridis partial IGS, 18S rRNA gene, I-DirI gene and partial ITS1
KeywordsRNA / Catalytic RNA / Lariat-capping ribozyme / Branching reaction / Lariat fold
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesDidymium iridis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsMeyer, M. / Nielsen, H. / Olieric, V. / Roblin, P. / Johansen, S.D. / Westhof, E. / Masquida, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BLAN-1502-02 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Speciation of a group I intron into a lariat capping ribozyme.
Authors: Meyer, M. / Nielsen, H. / Olieric, V. / Roblin, P. / Johansen, S.D. / Westhof, E. / Masquida, B.
History
DepositionApr 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Oct 4, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / refine_hist
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: Didymium iridis partial IGS, 18S rRNA gene, I-DirI gene and partial ITS1


Theoretical massNumber of molelcules
Total (without water)60,6291
Polymers60,6291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.560, 88.860, 105.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain Didymium iridis partial IGS, 18S rRNA gene, I-DirI gene and partial ITS1


Mass: 60628.977 Da / Num. of mol.: 1 / Fragment: 1502-1689 / Mutation: U140C / Source method: obtained synthetically / Source: (synth.) Didymium iridis (eukaryote) / References: GenBank: 62750861

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.85→28.55 Å / Num. all: 34494 / Num. obs: 5021 / % possible obs: 99.6 % / Redundancy: 6.87 % / Net I/σ(I): 9.63

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P95

4p95
PDB Unreleased entry


Resolution: 3.85→28.55 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 251 5.01 %
Rwork0.2455 --
obs0.2481 5010 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.85→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4014 0 0 4014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014490
X-RAY DIFFRACTIONf_angle_d0.8426997
X-RAY DIFFRACTIONf_dihedral_angle_d12.9182253
X-RAY DIFFRACTIONf_chiral_restr0.08940
X-RAY DIFFRACTIONf_plane_restr0.002188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.85-4.84670.40051220.33022320X-RAY DIFFRACTION99
4.8467-28.55370.26851290.22072439X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.9188 Å / Origin y: -0.5759 Å / Origin z: -16.7119 Å
111213212223313233
T1.6212 Å2-0.0984 Å2-0.1729 Å2-1.1925 Å2-0.0928 Å2--1.1305 Å2
L1.1789 °2-0.2632 °2-1.6798 °2-1.3925 °2-0.7456 °2--3.3798 °2
S-0.0001 Å °0.1041 Å °-0.1262 Å °-0.2339 Å °-0.2021 Å °0.0352 Å °-0.2573 Å °-0.03 Å °0.2015 Å °
Refinement TLS groupSelection details: all

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