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- PDB-6g7z: Lariat-capping ribozyme with a shortened DP2 stem loop -

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Basic information

Entry
Database: PDB / ID: 6g7z
TitleLariat-capping ribozyme with a shortened DP2 stem loop
Components(Lariat-capping ribozyme) x 2
KeywordsRNA / Lariat capping ribozyme
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesDidymium iridis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33594999571 Å
AuthorsMasquida, B. / Meyer, M. / Olieric, V.
Citation
Journal: Rna / Year: 2019
Title: Conformational adaptation of UNCG loops upon crowding.
Authors: Meyer, M. / Walbott, H. / Olieric, V. / Kondo, J. / Costa, M. / Masquida, B.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / 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 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lariat-capping ribozyme
B: Lariat-capping ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2095
Polymers59,9662
Non-polymers2443
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-33 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.945, 88.791, 110.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: RNA chain Lariat-capping ribozyme


Mass: 42567.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Didymium iridis (eukaryote)
#2: RNA chain Lariat-capping ribozyme


Mass: 17398.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Didymium iridis (eukaryote)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.63 % / Description: rod-like 50 ?m long
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM NaCl 100 mM HEPES pH 7.5 5-25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.33→44.4 Å / Num. obs: 108094 / % possible obs: 94.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 87.9280042935 Å2 / Net I/σ(I): 8.37
Reflection shellResolution: 3.3359→3.8184 Å / Num. unique obs: 2173

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Processing

Software
NameVersionClassification
REFMAC1.11rc1_2513refinement
PHENIX1.11rc1_2513refinement
XDSdata scaling
Cootmodel building
XDSdata reduction
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p8z

4p8z


Resolution: 3.33594999571→44.3955 Å / SU ML: 0.585939952286 / Cross valid method: FREE R-VALUE / σ(F): 2.00207155548 / Phase error: 41.5418750562
RfactorNum. reflection% reflection
Rfree0.30422432529 418 5.01319261214 %
Rwork0.234660832043 --
obs0.238474450676 8338 92.6547394155 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 77.3605845159 Å2
Refinement stepCycle: LAST / Resolution: 3.33594999571→44.3955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3970 25 0 3995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00270746614344462
X-RAY DIFFRACTIONf_angle_d0.7292096173286955
X-RAY DIFFRACTIONf_chiral_restr0.0356566880287929
X-RAY DIFFRACTIONf_plane_restr0.00310625878275186
X-RAY DIFFRACTIONf_dihedral_angle_d18.25002538132231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3359-3.81840.3853601684221150.3074542525032173X-RAY DIFFRACTION77.9557069847
3.8184-4.80990.2784966961481470.2710735595322804X-RAY DIFFRACTION99.662276258
4.8099-44.39940.2916117730161560.1954325345982943X-RAY DIFFRACTION99.8710924911
Refinement TLS params.Method: refined / Origin x: 18.2824686099 Å / Origin y: -1.52786626811 Å / Origin z: 18.1738677075 Å
111213212223313233
T0.402935683513 Å2-0.0652301546615 Å2-0.0228069546049 Å2-0.597097670431 Å2-0.0661382436584 Å2--0.445658257366 Å2
L1.77826242648 °20.90453229707 °20.198440002854 °2-1.62089046872 °2-0.117293136969 °2--2.86308240987 °2
S0.10492546927 Å °-0.415762829457 Å °0.210612583501 Å °0.222745534828 Å °-0.254833207211 Å °-0.0284080461667 Å °-0.120095931847 Å °0.498867441853 Å °0.121555167079 Å °
Refinement TLS groupSelection details: all

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