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- PDB-6qiv: Crystal structure of seleno-derivative CAG repeats with synthetic... -

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Basic information

Entry
Database: PDB / ID: 6qiv
TitleCrystal structure of seleno-derivative CAG repeats with synthetic CMBL4 compound
ComponentsRNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
KeywordsRNA / CAG repeats / CMBL / RNA complex with ligand
Function / homologyCMBL4 / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKiliszek, A. / Blaszczyk, L. / Rypniewski, W. / Nakatani, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Center for Research and Development (Poland)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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0822
Polymers2,5651
Non-polymers5181
Water181
1
A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,1644
Polymers5,1292
Non-polymers1,0352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)37.503, 37.503, 38.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n

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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.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-J4H / CMBL4


Mass: 517.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 mM MgCl2, Tacsimate and 5 mM hexamine cobalt chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.28→26.81 Å / Num. obs: 1430 / % possible obs: 99.8 % / Redundancy: 8.2 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.28→2.42 Å / Redundancy: 9 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 223 / CC1/2: 0.997 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QIQ

6qiq


Resolution: 2.28→26.8 Å / SU ML: 0.0797 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2672
RfactorNum. reflection% reflection
Rfree0.2537 143 10.02 %
Rwork0.1988 --
obs0.2046 1427 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.21 Å2
Refinement stepCycle: LAST / Resolution: 2.28→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 170 38 1 209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085232
X-RAY DIFFRACTIONf_angle_d1.6582351
X-RAY DIFFRACTIONf_chiral_restr0.054139
X-RAY DIFFRACTIONf_plane_restr0.007940
X-RAY DIFFRACTIONf_dihedral_angle_d12.2705134
LS refinement shellResolution: 2.28→26.81 Å
RfactorNum. reflection% reflection
Rfree0.2537 143 -
Rwork0.1988 1284 -
obs--99.65 %

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