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- PDB-4jrt: Crystal structure of an A-form RNA duplex containing three GU bas... -

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Basic information

Entry
Database: PDB / ID: 4jrt
TitleCrystal structure of an A-form RNA duplex containing three GU base pairs
Components
  • RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*GP*UP*GP*GP*UP*GP*CP*GP*GP*G)-3')
KeywordsRNA / A-form RNA / ribose-zipper motif / GU base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet
Authors: Kondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 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(P*GP*GP*GP*UP*GP*GP*UP*GP*CP*GP*GP*G)-3')
B: RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7032
Polymers7,7032
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.330, 29.330, 89.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 3979.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription
#2: RNA chain RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3')


Mass: 3723.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH (A 111) AND HOH (A 112) ARE CLOSED TO SYMMETRY-RELATED RNA MOLECULE.

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 7
Details: Sodium Cacodylate, Lithium acetate, PEG3350, pH 7.0, vapor diffusion, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorDetector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.6→20.7 Å / Num. obs: 2330

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
AMoREphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 353D

353d


Resolution: 2.6→20.7 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2275 220 9.4 %
Rwork0.1848 --
obs-2330 99.4 %
Solvent computationBsol: 41.7378 Å2
Displacement parametersBiso max: 113.1 Å2 / Biso mean: 76.1548 Å2 / Biso min: 41.68 Å2
Baniso -1Baniso -2Baniso -3
1-21.02 Å20 Å20 Å2
2--21.02 Å20 Å2
3----42.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 517 0 23 540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.195
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.5262
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.2682.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.690.4593220.3756211233100
2.69-2.80.3398250.3873198223100
2.8-2.930.4286260.3556225251100
2.93-3.080.3369150.2959203218100
3.08-3.280.287230.2167223246100
3.28-3.530.2602190.2351198217100
3.53-3.880.1995180.1689222240100
3.88-4.450.1901260.131421424099.2
4.45-5.60.1971220.1256212234100
5.6-1000.1843240.161220422894.6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ccc_xplor.param

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