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- PDB-5emf: Crystal structure of RNA r(GCUGCUGC) with antisense PNA p(GCAGCAGC) -

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Basic information

Entry
Database: PDB / ID: 5emf
TitleCrystal structure of RNA r(GCUGCUGC) with antisense PNA p(GCAGCAGC)
Components
  • RNA (5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3')
  • antisense PNA p(GCAGCAGC)
KeywordsRNA / CUG repeats / RNA/PNA duplex / antisense PNA / myotonic dystrophy type 1
Function / homologyPEP_NUC / RNA
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsKiliszek, A. / Banaszak, K. / Dauter, Z. / Rypniewski, W.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science CentreUMO-2011/01/B/NZ1/04429 Poland
Ministry of Science and Higher Education0450/IP1/2013/72 Poland
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: The first crystal structures of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches-toward anti-sense therapy against TREDs.
Authors: Kiliszek, A. / Banaszak, K. / Dauter, Z. / Rypniewski, W.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 17, 2017Group: Other
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,7944
Polymers4,7232
Non-polymers712
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-10 kcal/mol
Surface area3180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.110, 35.110, 69.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

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Components

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


Mass: 2518.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
#2: Peptide nucleic acid antisense PNA p(GCAGCAGC)


Mass: 2204.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 74.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200mM KCl, TRIS, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968681 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968681 Å / Relative weight: 1
ReflectionResolution: 1.14→30.41 Å / Num. obs: 18549 / % possible obs: 98.4 % / Redundancy: 9.8 % / Biso Wilson estimate: 16.135 Å2 / Rsym value: 0.051 / Net I/σ(I): 23.13
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→30.41 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.19 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15296 1109 6 %RANDOM
Rwork0.12171 ---
obs0.12361 17374 99.14 %-
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 mean: 14.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å2-0 Å2
2---0.4 Å20 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.14→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 166 160 114 440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.015442
X-RAY DIFFRACTIONr_bond_other_d0.0030.02253
X-RAY DIFFRACTIONr_angle_refined_deg2.5872.141648
X-RAY DIFFRACTIONr_angle_other_deg1.8183563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.241
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02359
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02130
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8961.218442
X-RAY DIFFRACTIONr_scbond_other1.8941.218443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0611.84648
X-RAY DIFFRACTIONr_long_range_B_refined3.79613.597742
X-RAY DIFFRACTIONr_long_range_B_other2.512.452679
X-RAY DIFFRACTIONr_rigid_bond_restr6.63695
X-RAY DIFFRACTIONr_sphericity_free23.588535
X-RAY DIFFRACTIONr_sphericity_bonded12.6975758
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 73 -
Rwork0.277 1142 -
obs--89.21 %

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