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- PDB-6gyv: Lariat-capping ribozyme (circular permutation form) -

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Basic information

Entry
Database: PDB / ID: 6gyv
TitleLariat-capping ribozyme (circular permutation form)
ComponentsLariat-capping ribozyme
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: 2.50003617357 Å
AuthorsMasquida, B. / Meyer, M. / Nielsen, H. / Olieric, V. / Roblin, P. / Johansen, S.D. / Westhof, E.
CitationJournal: 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
DepositionJul 2, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionAug 22, 2018ID: 4P95
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / exptl ...database_2 / exptl / 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lariat-capping ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1595
Polymers61,8921
Non-polymers2674
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-26 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 85.710, 108.530
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: 61891.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Didymium iridis (eukaryote)
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3,350 or (ii) 0.2 Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.6 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.5→47.83 Å / Num. obs: 34663 / % possible obs: 96.5 % / Redundancy: 7 % / Biso Wilson estimate: 46.1964978861 Å2 / Net I/σ(I): 3.16
Reflection shellResolution: 2.50003617357→2.589 Å

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Processing

Software
NameVersionClassification
PHENIX1.11rc1_2513refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p9r

4p9r


Resolution: 2.50003617357→47.8244954657 Å / SU ML: 0.399076274601 / Cross valid method: FREE R-VALUE / σ(F): 1.59236930785 / Phase error: 26.2237571904
RfactorNum. reflection% reflection
Rfree0.244903584028 1968 5.67752358423 %
Rwork0.198171132345 --
obs0.200698514255 34663 96.5032434088 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.2999933522 Å2
Refinement stepCycle: LAST / Resolution: 2.50003617357→47.8244954657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4054 26 88 4168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001643619384294605
X-RAY DIFFRACTIONf_angle_d0.5205962969057182
X-RAY DIFFRACTIONf_chiral_restr0.0228738097266959
X-RAY DIFFRACTIONf_plane_restr0.00243759276119192
X-RAY DIFFRACTIONf_dihedral_angle_d13.5821353442309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56260.3508063936621280.3110990500982289X-RAY DIFFRACTION94.4140625
2.5626-2.63180.3676492100041450.3076389981132277X-RAY DIFFRACTION94.7574334898
2.6318-2.70930.3421294173381730.2987875282952277X-RAY DIFFRACTION95.0349107836
2.7093-2.79670.4316770838671500.2904541083392292X-RAY DIFFRACTION95.5772994129
2.7967-2.89670.31301945781470.3005242498422315X-RAY DIFFRACTION95.6859696852
2.8967-3.01260.3630460073421410.2800973421372315X-RAY DIFFRACTION95.6386292835
3.0126-3.14970.2933705849161100.2236753180322355X-RAY DIFFRACTION96.4397496088
3.1497-3.31570.2841598265511260.2011393483052355X-RAY DIFFRACTION96.5369649805
3.3157-3.52340.2382389089961580.1957393647072337X-RAY DIFFRACTION96.9308469308
3.5234-3.79530.2018598445621630.1709776514142308X-RAY DIFFRACTION97.2451790634
3.7953-4.17710.2018881582281160.1557621955732399X-RAY DIFFRACTION97.3297213622
4.1771-4.7810.1854476715431420.1565553643042381X-RAY DIFFRACTION98.2476635514
4.781-6.02170.190500640581340.1548995462692401X-RAY DIFFRACTION98.4083850932
6.0217-47.83320.1923550367891350.1715782018252394X-RAY DIFFRACTION98.8276670574

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