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- PDB-4e6b: Crystal Structure of statistically disordered 19mer duplex p(CGG)... -

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Basic information

Entry
Database: PDB / ID: 4e6b
TitleCrystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3
Components(5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3') x 2
KeywordsRNA / siRNA / trinucleotide repeat expansion
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsMalinina, L. / Popov, A. / Tamjar, J.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2012
Title: Structural dynamics of double-helical RNAs composed of CUG/CUG- and CUG/CGG-repeats.
Authors: Tamjar, J. / Katorcha, E. / Popov, A. / Malinina, L.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
B: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
F: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
E: 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,0234
Polymers5,0234
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.779, 39.779, 34.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-102-

HOH

31A-106-

HOH

41B-102-

HOH

51B-103-

HOH

61B-104-

HOH

DetailsTHE BIOLOGICAL ASSEMBLY IS A 19-MER RNA DUPLEX. DUE TO STATISTICAL DISORDER WITHIN THE CRYSTAL, REMARK 350 REPRESENTS THE ASYMMETRIC UNIT.

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Components

#1: RNA chain 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Mass: 1255.818 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: obtained synthetically / Details: p(CGG)3C(CUG)3
#2: RNA chain 5'-R(P*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Mass: 1255.818 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: obtained synthetically / Details: p(CGG)3C(CUG)3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE CRYSTAL, RNA 19-MER P(CGG)3C(CUG)3 PACKS IN A PSEUDO-CONTINUOUS DOUBLE HELIX WITH A 4-BASE ...IN THE CRYSTAL, RNA 19-MER P(CGG)3C(CUG)3 PACKS IN A PSEUDO-CONTINUOUS DOUBLE HELIX WITH A 4-BASE ASYMMETRIC UNIT. TO BEST REPRESENT THE ARRANGEMENT OF THE BASES, THE RNA HAS BEEN MODELED AS TWO OVERLAPPING (WITH THE APPLICATION OF CRYSTAL SYMMETRY) SELF-COMPLEMENTARY TETRAMER DUPLEXES WITH OCCUPANCY 0.5.

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.9 mM ammonium sulfate, 5% isopropanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 3488 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.259 / Net I/σ(I): 24.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.47-1.52.10.1691691.176197.1
1.5-1.522.20.1441791.0171100
1.52-1.552.30.1251710.8371100
1.55-1.582.20.0871760.9031100
1.58-1.622.20.091721.1921100
1.62-1.662.20.071770.933198.9
1.66-1.72.30.0641710.969198.8
1.7-1.742.20.0451680.903197.1
1.74-1.792.30.0481701.0011100
1.79-1.852.20.0431850.8151100
1.85-1.922.30.0321780.728199.4
1.92-1.992.10.0281740.829199.4
1.99-2.092.30.0291640.994199.4
2.09-2.22.30.0291840.7421100
2.2-2.332.30.0261800.8781100
2.33-2.512.30.0421761.5771100
2.51-2.772.20.041672.381199.4
2.77-3.176.10.0711751.941198.3
3.17-3.9912.50.0531741.335199.4
3.99-3011.80.0451781.2681100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.2611 / WRfactor Rwork: 0.2469 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.7923 / SU R Cruickshank DPI: 0.134 / SU Rfree: 0.1082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 152 4.4 %RANDOM
Rwork0.2043 ---
obs0.2048 3481 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.28 Å2 / Biso mean: 31.9728 Å2 / Biso min: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.47→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 344 0 18 362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021382
X-RAY DIFFRACTIONr_bond_other_d00.02128
X-RAY DIFFRACTIONr_angle_refined_deg1.8593592
X-RAY DIFFRACTIONr_angle_other_deg1.6733336
X-RAY DIFFRACTIONr_chiral_restr0.0710.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02168
X-RAY DIFFRACTIONr_gen_planes_other0.0120.0232
X-RAY DIFFRACTIONr_nbd_refined0.060.214
X-RAY DIFFRACTIONr_nbd_other0.1920.2106
X-RAY DIFFRACTIONr_nbtor_refined0.2390.2137
X-RAY DIFFRACTIONr_nbtor_other0.0590.282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0310.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5280.22
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0050.21
X-RAY DIFFRACTIONr_scbond_it1.3293382
X-RAY DIFFRACTIONr_scangle_it1.9034.5592
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 13 -
Rwork0.258 247 -
all-260 -
obs--98.48 %

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