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- PDB-3glp: 1.23 A resolution X-ray structure of (GCUGCUGC)2 -

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Basic information

Entry
Database: PDB / ID: 3glp
Title1.23 A resolution X-ray structure of (GCUGCUGC)2
Components5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'
KeywordsRNA / stretched U-U wobble / myotonic dystrophy / CUG repeats
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.23 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy.
Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 11, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / ndb_struct_conf_na ...diffrn_source / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _ndb_struct_na_base_pair.propeller ..._diffrn_source.pdbx_synchrotron_site / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.tilt / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,8778
Polymers12,5935
Non-polymers2843
Water3,495194
1
A: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'
B: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2254
Polymers5,0372
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-18 kcal/mol
Surface area3130 Å2
MethodPISA
2
C: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'
D: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1333
Polymers5,0372
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-18 kcal/mol
Surface area3150 Å2
MethodPISA
3
E: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'

E: 5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,0372
Polymers5,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area780 Å2
ΔGint-9 kcal/mol
Surface area3120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.96, 38.85, 77.72
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 2518.537 Da / Num. of mol.: 5 / Source method: obtained synthetically
Details: Synthetic mRNA with the sequence of the part of human mRNA
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MgCl2, Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium chloride11
2Lithium sulfate11
3Magnesium chloride12
4Lithium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 19.8 / Number: 224476 / Rmerge(I) obs: 0.058 / Χ2: 1.01 / D res high: 1.23 Å / D res low: 20 Å / Num. obs: 62090 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.332095.410.0521.0074
2.653.3397.610.0540.9874.9
2.312.6510010.0531.075.1
2.12.3110010.0561.0375.1
1.952.110010.0581.0494.5
1.841.9599.810.0591.0223.3
1.751.8499.910.0611.0133.3
1.671.7599.710.0611.0063.3
1.61.6799.710.070.9843.3
1.551.699.510.0811.0183.3
1.51.5599.610.0981.0173.3
1.461.599.310.1160.9813.2
1.421.4699.410.1411.0043.3
1.391.4299.210.1641.0053.3
1.351.3999.110.1891.0063.3
1.321.359910.2081.0233.2
1.31.329910.2281.0033.3
1.271.398.510.2470.9693.2
1.251.2798.710.2880.9623.2
1.231.2597.610.2981.0543.1
ReflectionResolution: 1.23→20 Å / Num. all: 32055 / Num. obs: 32055 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.058 / Net I/σ(I): 21.3
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 1502 / Rsym value: 0.3 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å18.62 Å
Translation2.5 Å18.62 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-RNA model

Resolution: 1.23→17.98 Å / Cor.coef. Fo:Fc: 0.974 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.92 / SU B: 1.049 / SU ML: 0.021 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1602 -random
Rwork0.147 ---
all0.184 31664 --
obs0.148 30062 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.46 Å2 / Biso mean: 22.8 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.3 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.042 Å
Luzzati sigma a-0.021 Å
Refinement stepCycle: LAST / Resolution: 1.23→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 830 16 194 1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211053
X-RAY DIFFRACTIONr_angle_refined_deg2.74931641
X-RAY DIFFRACTIONr_chiral_restr0.1490.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02441
X-RAY DIFFRACTIONr_nbd_refined0.2060.2401
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.239
X-RAY DIFFRACTIONr_scbond_it3.41831453
X-RAY DIFFRACTIONr_scangle_it4.0084.51639
X-RAY DIFFRACTIONr_rigid_bond_restr2.66131453
X-RAY DIFFRACTIONr_sphericity_free12.1273204
X-RAY DIFFRACTIONr_sphericity_bonded9.173950
LS refinement shellResolution: 1.23→1.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 107 -
Rwork0.186 2293 -
obs-2187 97.99 %

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