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- PDB-4u37: Native 7mer-RNA duplex -

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Basic information

Entry
Database: PDB / ID: 4u37
TitleNative 7mer-RNA duplex
Components
  • RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
KeywordsRNA / RNA duplex
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSheng, J. / Larsen, A. / Heuberger, B. / Blain, J.C. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs.
Authors: Sheng, J. / Larsen, A. / Heuberger, B.D. / Blain, J.C. / Szostak, J.W.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Oct 15, 2014Group: Database references
Revision 1.5Jan 14, 2015Group: Database references
Revision 1.6Aug 26, 2015Group: Data collection
Revision 1.7Sep 27, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.8Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.9Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4182
Polymers4,4182
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area2750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.478, 38.490, 30.408
Angle α, β, γ (deg.)90.00, 110.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

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Components

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


Mass: 2157.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')


Mass: 2260.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% MPD, 40 mM Na cacodylate pH 6.0, 12 mM spermine tetra-HCl and 80 mM NaCl

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 5625 / Num. obs: 5375 / % possible obs: 95.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.124 / Rsym value: 0.11 / Net I/σ(I): 12.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.35 / % possible all: 73.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 434D

434d


Resolution: 1.55→28.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.795 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22796 250 4.4 %RANDOM
Rwork0.20263 ---
obs0.20385 5375 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.18 Å2
2--0.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.55→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 292 0 44 336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.441503
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.0770.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.02144
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.592 Å
RfactorNum. reflection% reflection
Rfree0.204 16 -
Rwork0.163 271 -
obs--66.59 %

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