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- PDB-4e59: Crystal structure of GCCGCCGC duplex -

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Basic information

Entry
Database: PDB / ID: 4.0E+59
TitleCrystal structure of GCCGCCGC duplex
ComponentsRNA duplex containing CCG repeats
KeywordsRNA / 3' slippery duplexes / X-linked mental retardation / Huntington's disease / myotonic dystrophy type 1 / CCG repeats
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystallographic characterization of CCG repeats.
Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.name
Revision 1.2Sep 13, 2023Group: 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 duplex containing CCG repeats
B: RNA duplex containing CCG repeats


Theoretical massNumber of molelcules
Total (without water)5,0332
Polymers5,0332
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-4 kcal/mol
Surface area3060 Å2
MethodPISA
2
A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats

A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats

A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats


Theoretical massNumber of molelcules
Total (without water)15,0996
Polymers15,0996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3640 Å2
ΔGint-46 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 40.580, 56.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

21A-106-

HOH

31B-105-

HOH

41B-106-

HOH

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Components

#1: RNA chain RNA duplex containing CCG repeats


Mass: 2516.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is a part of mRNA in humans / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.77 Å3/Da / Density % sol: 30.41 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: magnesium acetate, MES and ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. all: 5101 / Num. obs: 5101 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.04 / Net I/σ(I): 26.14
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 262 / Rsym value: 0.711 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+58 / Resolution: 1.54→18.715 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3035 501 100 %RANDOM
Rwork0.2553 ---
all0.257 5073 --
obs0.2553 5073 99.41 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.918 Å2 / ksol: 0.458 e/Å3
Displacement parametersBiso mean: 27.79 Å2
Baniso -1Baniso -2Baniso -3
1-4.8628 Å20 Å2-0 Å2
2--4.8628 Å2-0 Å2
3----9.7256 Å2
Refinement stepCycle: LAST / Resolution: 1.54→18.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 300 0 16 316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332
X-RAY DIFFRACTIONf_angle_d1.29516
X-RAY DIFFRACTIONf_dihedral_angle_d13.993164
X-RAY DIFFRACTIONf_chiral_restr0.07670
X-RAY DIFFRACTIONf_plane_restr0.01514
LS refinement shellResolution: 1.54→1.695 Å
RfactorNum. reflection% reflection
Rfree0.3627 130 -
Rwork0.3411 161 -
obs-1270 100 %

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