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- PDB-4u34: Crystal Structures of RNA Duplexes Containing 2-thio-Uridine -

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Basic information

Entry
Database: PDB / ID: 4u34
TitleCrystal Structures of RNA Duplexes Containing 2-thio-Uridine
Components
  • RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*(SUR)P*CP*C-3')
KeywordsRNA / 2-thio-uridine
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.2Oct 1, 2014Group: Database references
Revision 1.3Oct 15, 2014Group: Database references
Revision 1.4Jan 14, 2015Group: Database references
Revision 1.5Aug 26, 2015Group: Data collection
Revision 1.6Sep 27, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.7Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Sep 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4342
Polymers4,4342
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-1 kcal/mol
Surface area2630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.385, 38.683, 30.072
Angle α, β, γ (deg.)90.00, 109.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 2173.397 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.: 97 / 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: 49.7 %
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: 1.35→30 Å / Num. all: 8436 / Num. obs: 8031 / % possible obs: 93.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 11.1 / % possible all: 66.6

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Processing

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

434d


Resolution: 1.35→22.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.725 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19788 404 4.8 %RANDOM
Rwork0.18756 ---
obs0.18807 8031 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.35→22.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 292 0 97 389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.012325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.538503
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_restr0.080.256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02144
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: 1.347→1.381 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 23 -
Rwork0.259 373 -
obs--61.68 %
Refinement TLS params.

T12: -0.0048 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20790.7771-0.0840.67240.25760.58910.0209-0.0746-0.0114-0.0121-0.0426-0.0041-0.0393-0.02290.02170.0242-0.00580.0501-0.00420.036-2.0012-3.1276-9.4296
20.40630.1384-0.30731.60791.18421.30150.0388-0.0013-0.0502-0.0503-0.0455-0.0488-0.0743-0.05010.00670.0285-0.01020.03540.01750.0283-4.28651.9318-11.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2B8 - 14

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