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- PDB-6bjx: Group I self-splicing intron P4-P6 domain mutant U131A (with isop... -

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Basic information

Entry
Database: PDB / ID: 6bjx
TitleGroup I self-splicing intron P4-P6 domain mutant U131A (with isopropanol soaking)
ComponentsGroup I self-splicing intron P4-P6 domain
KeywordsRNA / ribozyme
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 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
DepositionNov 7, 2017Deposition 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Group I self-splicing intron P4-P6 domain
B: Group I self-splicing intron P4-P6 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63522
Polymers102,1492
Non-polymers48620
Water00
1
A: Group I self-splicing intron P4-P6 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31711
Polymers51,0741
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group I self-splicing intron P4-P6 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31711
Polymers51,0741
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.670, 130.010, 146.410
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 P4-P6 domain


Mass: 51074.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) / References: GenBank: 345541658
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
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: 3.14→63.8 Å / Num. obs: 25244 / % possible obs: 98.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 113.088043928 Å2 / Net I/σ(I): 16.3

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Processing

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

1gid


Resolution: 3.14→63.8 Å / SU ML: 0.349042001144 / Cross valid method: FREE R-VALUE / σ(F): 1.32948920372 / Phase error: 29.7701007419
RfactorNum. reflection% reflection
Rfree0.22924417573 2520 9.99524036173 %
Rwork0.211184378342 --
obs0.213003674255 25212 98.7466708444 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 128.619241904 Å2
Refinement stepCycle: LAST / Resolution: 3.14→63.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6770 20 0 6790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003006556613997580
X-RAY DIFFRACTIONf_angle_d0.63335565445211818
X-RAY DIFFRACTIONf_chiral_restr0.04168612744561580
X-RAY DIFFRACTIONf_plane_restr0.00398600576193316
X-RAY DIFFRACTIONf_dihedral_angle_d15.01619216133786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1426-3.20310.5035908066191170.3635851116481054X-RAY DIFFRACTION83.7625178827
3.2031-3.26850.3177172763681410.3108028264971261X-RAY DIFFRACTION99.4326241135
3.2685-3.33950.3285173787451370.289910559841237X-RAY DIFFRACTION99.6374184191
3.3395-3.41720.2877070818131410.2880611714541264X-RAY DIFFRACTION99.7161107168
3.4172-3.50270.2906768638891360.2658885042061244X-RAY DIFFRACTION99.5670995671
3.5027-3.59740.2443111260991360.2398185808791242X-RAY DIFFRACTION99.5664739884
3.5974-3.70320.2310139059151400.228489214861256X-RAY DIFFRACTION99.9284180387
3.7032-3.82270.2172975274631410.2082904449061261X-RAY DIFFRACTION99.5031937544
3.8227-3.95930.2053929984561400.2128664509061268X-RAY DIFFRACTION99.716713881
3.9593-4.11780.2551918562161390.2106553763921255X-RAY DIFFRACTION99.9283154122
4.1178-4.30520.233400052091410.2218951911521260X-RAY DIFFRACTION99.6443812233
4.3052-4.53210.2133163331251400.2129722639411261X-RAY DIFFRACTION99.6443812233
4.5321-4.8160.2382025058011420.1941341046131276X-RAY DIFFRACTION99.6486296557
4.816-5.18770.1933794691391420.1746535585921274X-RAY DIFFRACTION99.8589562764
5.1877-5.70940.2009092249721440.1821493605111298X-RAY DIFFRACTION99.9306999307
5.7094-6.53490.1972002081431450.1954509324411299X-RAY DIFFRACTION99.6549344375
6.5349-8.23050.1976998078291440.1976082015141303X-RAY DIFFRACTION98.9740082079
8.2305-63.80120.2443537294841540.2114651470821379X-RAY DIFFRACTION99.2875647668

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