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- PDB-4e58: Crystal structure of GCC(LCG)CCGC duplex containing LNA residue -

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Basic information

Entry
Database: PDB / ID: 4.0E+58
TitleCrystal structure of GCC(LCG)CCGC duplex containing LNA residue
ComponentsRNA duplex containing CCG repeats
KeywordsRNA / CCG repeats / 5' slippery duplexes / X-linked mental retardation / Huntington's disease / myotonic dystrophy type 1 / LNA Guanosine
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, R.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: RNA duplex containing CCG repeats
E: RNA duplex containing CCG repeats
D: RNA duplex containing CCG repeats
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7785
Polymers7,5863
Non-polymers1922
Water25214
1
C: RNA duplex containing CCG repeats
D: RNA duplex containing CCG repeats
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2494
Polymers5,0572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-27 kcal/mol
Surface area2840 Å2
MethodPISA
2
E: RNA duplex containing CCG repeats

E: RNA duplex containing CCG repeats


Theoretical massNumber of molelcules
Total (without water)5,0572
Polymers5,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area1750 Å2
ΔGint6 kcal/mol
Surface area2820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.016, 42.016, 81.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11D-203-

HOH

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Components

#1: RNA chain RNA duplex containing CCG repeats


Mass: 2528.579 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Similar sequences occur in mRNA in humans / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MES, MgCl2 and Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9148 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9148 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 5762 / Num. obs: 5762 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.3 % / Biso Wilson estimate: 50.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 23.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 2.175 / Num. unique all: 273 / Rsym value: 0.673 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GLP

3glp


Resolution: 1.952→18.79 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3008 562 100 %RANDOM
Rwork0.258 ---
all0.258 5717 --
obs0.258 5717 99.46 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.22 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 49.43 Å2
Baniso -1Baniso -2Baniso -3
1-6.3525 Å2-0 Å20 Å2
2--6.3525 Å2-0 Å2
3----12.705 Å2
Refinement stepCycle: LAST / Resolution: 1.952→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 10 14 510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01549
X-RAY DIFFRACTIONf_angle_d1.23856
X-RAY DIFFRACTIONf_dihedral_angle_d16.246252
X-RAY DIFFRACTIONf_chiral_restr0.066110
X-RAY DIFFRACTIONf_plane_restr0.01223
LS refinement shellResolution: 1.952→2.1486 Å
RfactorNum. reflection% reflection
Rfree0.4417 129 -
Rwork0.3766 179 -
obs-1238 97 %

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