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- PDB-6d8o: Group I self-splicing intron P4-P6 domain mutant A230U -

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Basic information

Entry
Database: PDB / ID: 6d8o
TitleGroup I self-splicing intron P4-P6 domain mutant A230U
ComponentsGroup I self-splicing intron
KeywordsRNA / ribozyme
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80112483119 Å
AuthorsShoffner, G.M.
CitationJournal: Structure / Year: 2018
Title: In Crystallo Selection to Establish New RNA Crystal Contacts.
Authors: Shoffner, G.M. / Wang, R. / Podell, E. / Cech, T.R. / Guo, F.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 4, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group I self-splicing intron
B: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,51821
Polymers102,0572
Non-polymers46219
Water00
1
A: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,24710
Polymers51,0281
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,27111
Polymers51,0281
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.250, 129.490, 146.130
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 Group I self-splicing intron


Mass: 51028.281 Da / Num. of mol.: 2 / Fragment: P4-P6 domain / Mutation: A230U / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) / References: GenBank: 10832
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg

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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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 1000, sodium cacodylate, spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→63.6 Å / Num. obs: 35173 / % possible obs: 99.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 97.8791369622 Å2 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gid

1gid


Resolution: 2.80112483119→59.1950080889 Å / SU ML: 0.387070124828 / Cross valid method: FREE R-VALUE / σ(F): 1.35632426171 / Phase error: 29.5202997819
RfactorNum. reflection% reflection
Rfree0.22642770118 1762 5.01465691436 %
Rwork0.210847551416 --
obs0.21162944016 35137 99.1702181705 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 112.264467942 Å2
Refinement stepCycle: LAST / Resolution: 2.80112483119→59.1950080889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6762 19 0 6781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001540618799957568
X-RAY DIFFRACTIONf_angle_d0.45007392166411798
X-RAY DIFFRACTIONf_chiral_restr0.02371908720031580
X-RAY DIFFRACTIONf_plane_restr0.00186059747993316
X-RAY DIFFRACTIONf_dihedral_angle_d13.817941563786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8011-2.87690.3858388021591190.4358035152332357X-RAY DIFFRACTION91.0628907687
2.8769-2.96150.457014635481440.3730543443412516X-RAY DIFFRACTION99.9248685199
2.9615-3.05710.3216589567811360.3092297141812526X-RAY DIFFRACTION99.7751124438
3.0571-3.16640.3130156318581330.263411528252562X-RAY DIFFRACTION99.8888065234
3.1664-3.29310.2807048669121190.2499177449772560X-RAY DIFFRACTION99.9626865672
3.2931-3.4430.3010989870531160.2360612451822569X-RAY DIFFRACTION99.9255675475
3.443-3.62450.2416085947261510.2223217600312550X-RAY DIFFRACTION99.8890532544
3.6245-3.85150.2348123527051310.200761039072583X-RAY DIFFRACTION99.8161088636
3.8515-4.14880.2322601916411380.1942339124772592X-RAY DIFFRACTION99.8902305159
4.1488-4.56620.1954532579651350.189706364292582X-RAY DIFFRACTION99.8529952223
4.5662-5.22660.1904474647211530.169522063482591X-RAY DIFFRACTION99.8907899527
5.2266-6.58360.2007930609571440.1872530297242625X-RAY DIFFRACTION99.8197548666
6.5836-59.20820.2099932944631430.2152787374182762X-RAY DIFFRACTION99.5544893763

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