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- PDB-3gm7: 1.58 A resolution X-ray structure of (CUG)6 -

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Basic information

Entry
Database: PDB / ID: 3gm7
Title1.58 A resolution X-ray structure of (CUG)6
Components5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
KeywordsRNA / stretched U-U wobble / myotonic dystrophy / CUG repeats
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / PDB entry 1ZEV / Resolution: 1.58 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The structural basis of myotonic dystrophy from the crystal structure of CUG repeats.
Authors: Mooers, B.H. / Logue, J.S. / Berglund, J.A.
History
DepositionMar 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY (3GM7) REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURE (PDB ID 1ZEV) ...THIS ENTRY (3GM7) REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURE (PDB ID 1ZEV) DETERMINED BY THE AUTHORS: B.H. MOOERS, J.S. LOGUE, J.A. BERGLUND

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: 5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
H: 5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)11,3892
Polymers11,3892
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-15.2 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.102, 39.102, 141.277
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
11G-20-

HOH

21G-21-

HOH

31G-38-

HOH

41G-39-

HOH

51G-40-

HOH

61H-20-

HOH

71H-28-

HOH

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Components

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


Mass: 5694.363 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic mRNA with the sequence of the part of human mRNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, NaCl, MgCl2, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MOPS11
2Sodium chloride11
3Magnesium chloride11
4MPD11
5MOPS12
6Sodium chloride12
7Magnesium chloride12
8MPD12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementMethod to determine structure: PDB entry 1ZEV / Resolution: 1.58→19.6 Å / Cross valid method: THROUGHOUT
Details: AUTHORS STATE THAT ALL THE ATOMS THAT ARE LISTED IN REMARK 500 FIT WELL THE ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.262 1084 -
Rwork0.219 --
obs0.227 9925 99.6 %
all-11009 -
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 750 0 52 802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.34
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_approx_iso_adps0.074
LS refinement shellResolution: 1.58→1.64 Å
RfactorNum. reflection% reflection
Rwork0.267 --
Rfree-103 -
obs-1169 90.6 %

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