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- PDB-422d: 5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3' -

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Basic information

Entry
Database: PDB / ID: 422d
Title5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'
Components5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'
KeywordsRNA / DOUBLE HELIX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEswaramoorthy, S. / Rao, S.T. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the dodecamer r(GAUCACUUCGGU) with four 5'-overhang nucleotides.
Authors: Eswaramoorthy, S. / Rao, S.T. / Pan, B. / Sundaralingam, M.
History
DepositionSep 10, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,5792
Polymers7,5792
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.34, 39.98, 32.47
Angle α, β, γ (deg.)90.00, 104.7, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 3789.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.04 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1dropKCl
20.1 Mmagnesium acetate1drop
30.6 mMspermine1drop
40.05 Msodium cacodylate1droppH6.5
510 %PEG80001drop
620 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorDetector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→10 Å / Num. all: 2742 / Num. obs: 2494 / % possible obs: 91 % / Observed criterion σ(F): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.6→2.76 Å / Mean I/σ(I) obs: 2.1 / % possible all: 71
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 91 %
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 71 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLORmodel building
X-PLOR3.1refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OCTAMER SEGMENT FROM 14-MER AUAUAUAUAUAUAU

Resolution: 2.6→10 Å / Rfactor Rfree error: 0.018 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.188 163 6 %RANDOM
Rwork0.188 ---
all0.188 2742 --
obs-2494 91 %-
Displacement parametersBiso mean: 10.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 500 0 27 527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d7.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.321.5
X-RAY DIFFRACTIONx_mcangle_it3.362
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.123 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.324 339 -
Rfree-17 4.8 %
obs--80 %
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg7.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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