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- PDB-3syw: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Rev... -

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Basic information

Entry
Database: PDB / ID: 3syw
TitleCrystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations
ComponentsRNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
KeywordsRNA / CUG repeat RNA / A-form RNA / Myotonic dystrophy / Internal loop
Function / homologyPHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsKumar, A. / Park, H. / Pengfei, F. / Parkesh, R. / Guo, M. / Nettles, K.W. / Disney, M.D.
CitationJournal: Biochemistry / Year: 2011
Title: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations
Authors: Kumar, A. / Park, H. / Fang, P. / Parkesh, R. / Guo, M. / Nettles, K.W. / Disney, M.D.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2694
Polymers12,0792
Non-polymers1902
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-21 kcal/mol
Surface area6410 Å2
MethodPISA
2
A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
hetero molecules

A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
hetero molecules

A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,80712
Polymers36,2376
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9900 Å2
ΔGint-120 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.535, 46.535, 135.001
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-20-

PO4

21B-20-

PO4

31A-21-

HOH

41A-27-

HOH

51A-31-

HOH

61A-32-

HOH

71B-22-

HOH

81B-23-

HOH

91B-24-

HOH

101B-40-

HOH

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Components

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


Mass: 6039.569 Da / Num. of mol.: 2 / Fragment: RNA / Source method: obtained synthetically / Details: Polyribonucleotide
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Details: Polyribonucleotide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / pH: 6
Details: 15 mM magnesium acetate, 50 mM sodium cacodylate, pH 6.0, 1.7 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97855
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 9, 2011 / Details: RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.52→34.6 Å / Num. obs: 16712 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.057 / Net I/σ(I): 48.99
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.1 / % possible all: 98.9

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→34.6 Å / σ(F): 0.15
RfactorNum. reflection% reflection
Rfree0.187 805 5.01 %
Rwork0.167 --
obs0.168 16068 -
all-16712 -
Refinement stepCycle: LAST / Resolution: 1.57→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 796 10 176 982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008998
X-RAY DIFFRACTIONf_angle_d0.9821558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5199-1.61510.209600.21430X-RAY DIFFRACTION1
1.6151-1.73980.161900.15180X-RAY DIFFRACTION1
1.7398-1.91490.158600.1460X-RAY DIFFRACTION1
1.9149-2.19190.175200.16820X-RAY DIFFRACTION1
2.1919-2.76140.202800.1680X-RAY DIFFRACTION1
2.7614-34.61140.191600.16770X-RAY DIFFRACTION1

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