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- PDB-6qit: Crystal structure of CAG repeats with synthetic CMBL3b compound -

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Basic information

Entry
Database: PDB / ID: 6qit
TitleCrystal structure of CAG repeats with synthetic CMBL3b compound
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 / Resolution: 1.501 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Water3,153175
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)35.233, 50.989, 39.554
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 175 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20 mM magnesium acetate and 1.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→29.3 Å / Num. obs: 20979 / % possible obs: 96.1 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3317 / CC1/2: 0.65 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.501→29.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1049 5.01 %
Rwork0.1504 --
obs0.1527 20920 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 680 148 175 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009957
X-RAY DIFFRACTIONf_angle_d1.4841453
X-RAY DIFFRACTIONf_dihedral_angle_d11.336582
X-RAY DIFFRACTIONf_chiral_restr0.069164
X-RAY DIFFRACTIONf_plane_restr0.01186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5013-1.58040.28551460.21622764X-RAY DIFFRACTION94
1.5804-1.67940.2481490.16932820X-RAY DIFFRACTION96
1.6794-1.80910.22021500.15552841X-RAY DIFFRACTION96
1.8091-1.99110.23561490.1422833X-RAY DIFFRACTION97
1.9911-2.27910.18151510.1522872X-RAY DIFFRACTION97
2.2791-2.87110.23651530.17752893X-RAY DIFFRACTION97
2.8711-29.30570.15531510.13042848X-RAY DIFFRACTION95

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