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- PDB-4e48: Structure of 20mer double-helical RNA composed of CUG/CUG-repeats -

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Basic information

Entry
Database: PDB / ID: 4.0E+48
TitleStructure of 20mer double-helical RNA composed of CUG/CUG-repeats
Components5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
KeywordsRNA / siRNA / trinucleotide repeat expansion
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKatorcha, E. / Malinina, L.
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 12, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
B: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
D: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,59310
Polymers19,0343
Non-polymers5597
Water1,69394
1
A: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
B: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1528
Polymers12,6902
Non-polymers4626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-77 kcal/mol
Surface area7360 Å2
MethodPISA
2
D: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules

D: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8824
Polymers12,6902
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2360 Å2
ΔGint-53 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.642, 43.642, 158.556
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-102-

SO4

21A-102-

SO4

31A-103-

K

41A-104-

K

51A-203-

HOH

61A-211-

HOH

71A-214-

HOH

81A-216-

HOH

91A-240-

HOH

101A-241-

HOH

111B-205-

HOH

121B-209-

HOH

131B-213-

HOH

141B-223-

HOH

151B-230-

HOH

161B-231-

HOH

171B-237-

HOH

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Components

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


Mass: 6344.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: pG(CUG)6C
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.6 mM ammonium sulfate, 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2008
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 6607 / Num. obs: 6468 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.3 / Num. unique all: 175 / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 9.54 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.8 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 307 4.8 %RANDOM
Rwork0.2033 ---
obs0.2067 6442 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 24.9698 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1266 27 94 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211424
X-RAY DIFFRACTIONr_bond_other_d0.0030.02498
X-RAY DIFFRACTIONr_angle_refined_deg1.55332214
X-RAY DIFFRACTIONr_angle_other_deg1.01531296
X-RAY DIFFRACTIONr_chiral_restr0.050.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_nbd_refined0.1240.2170
X-RAY DIFFRACTIONr_nbd_other0.230.2674
X-RAY DIFFRACTIONr_nbtor_refined0.2250.2561
X-RAY DIFFRACTIONr_nbtor_other0.0660.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.237
X-RAY DIFFRACTIONr_scbond_it0.90831500
X-RAY DIFFRACTIONr_scangle_it1.3414.52214
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 31 -
Rwork0.284 402 -
all-433 -
obs--91.74 %

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