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- PDB-6qir: Crystal structure of CAG repeats with synthetic CMBL3a compound (... -

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Basic information

Entry
Database: PDB / ID: 6qir
TitleCrystal structure of CAG repeats with synthetic CMBL3a compound (model I)
ComponentsRNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
KeywordsRNA / CAG repeats / CMBL / RNA complex with ligand
Function / homologyCMBL3a / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 Å
AuthorsKiliszek, A. / Blaszczyk, L. / Rypniewski, W. / Nakatani, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
NCN 2017/26/E/NZ1/00950 Poland
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Authors: Mukherjee, S. / Blaszczyk, L. / Rypniewski, W. / Falschlunger, C. / Micura, R. / Murata, A. / Dohno, C. / Nakatani, K. / Kiliszek, A.
History
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
B: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
C: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
D: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2618
Polymers10,2584
Non-polymers2,0024
Water2,504139
1
A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
B: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1304
Polymers5,1292
Non-polymers1,0012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
D: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1304
Polymers5,1292
Non-polymers1,0012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.024, 46.747, 54.811
Angle α, β, γ (deg.)90.00, 129.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain
RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')


Mass: 2564.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-J48 / CMBL3a


Mass: 500.529 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H26N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10mM MgCl2 and 1M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9171 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9171 Å / Relative weight: 1
ReflectionResolution: 1.53→42.158 Å / Num. obs: 43700 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.9
Reflection shellResolution: 1.53→1.62 Å / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6954 / CC1/2: 0.872 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QIQ

6qiq


Resolution: 1.531→42.158 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.61
RfactorNum. reflection% reflection
Rfree0.2327 1043 4.7 %
Rwork0.1768 --
obs0.1793 22183 97.66 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å
Refinement stepCycle: LAST / Resolution: 1.531→42.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 680 148 139 967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01924
X-RAY DIFFRACTIONf_angle_d1.4561400
X-RAY DIFFRACTIONf_dihedral_angle_d10.346532
X-RAY DIFFRACTIONf_chiral_restr0.064156
X-RAY DIFFRACTIONf_plane_restr0.01180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5313-1.61210.51011480.44792975X-RAY DIFFRACTION95
1.6121-1.71310.32231470.30232876X-RAY DIFFRACTION95
1.7131-1.84530.26841760.21962989X-RAY DIFFRACTION98
1.8453-2.0310.25411640.1833030X-RAY DIFFRACTION99
2.031-2.32490.26621240.1683090X-RAY DIFFRACTION100
2.3249-2.9290.27041260.2143097X-RAY DIFFRACTION99
2.929-42.17410.19361580.1423083X-RAY DIFFRACTION98

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