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- PDB-280d: THE STRUCTURE OF AN RNA DODECAMER SHOWS HOW TANDEM U-U BASE PAIRS... -

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Basic information

Entry
Database: PDB / ID: 280d
TitleTHE STRUCTURE OF AN RNA DODECAMER SHOWS HOW TANDEM U-U BASE PAIRS INCREASE THE RANGE OF STABLE RNA STRUCTURES AND THE DIVERSITY OF RECOGNITION SITES
ComponentsRNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')
KeywordsRNA / UNUSUAL RNA / DOUBLE HELIX / INTERNAL LOOP / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLietzke, S.E. / Barnes, C.L. / Kundrot, C.E.
Citation
Journal: Structure / Year: 1996
Title: The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites.
Authors: Lietzke, S.E. / Barnes, C.L. / Berglund, J.A. / Kundrot, C.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Data reduction from twinned RNA crystals
Authors: Lietzke, S.E. / Carperos, V.E. / Kundrot, C.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystallization of Ribozymes and Small RNA Motifs by a Sparse Matrix Approach
Authors: Doudna, J.A. / Grosshans, C. / Gooding, A. / Kundrot, C.E.
History
DepositionAug 22, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 30, 1996Provider: repository / Type: Initial release
Revision 1.1May 23, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,2814
Polymers15,2814
Non-polymers00
Water2,846158
1
A: RNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')
B: RNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,6412
Polymers7,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')
D: RNA (5'-R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,6412
Polymers7,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.440, 28.910, 46.460
Angle α, β, γ (deg.)98.87, 72.95, 96.16
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3820.296 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Description: THE DODECAMER WAS PREPARED BY TRANSCRIPTION WITH T7 RNA POLYMERASE FROM A SINGLE STRANDED DNA TEMPLATE.
Plasmid: PAR1219 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Description: THE CRYSTALS WERE TWINNED; DATA FROM EACH LATTICE WAS INDIVIDUALLY PROCESSED WITH XDS AND A SET OF PROGRAMS DESCRIBED IN REFERENCE 1. DATA FROM THE TWO LATTICES WERE THEN MERGED WITH XSCALE.
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5NH4 ACETATE11
6WATER12
7MPD12
8MGCL212
9NA CACODYLATE12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.63 mg/mlRNA1drop
212.5 mM1dropMgCl2
325 mMsodium cacodylate1drop
42.5 %MPD1dropor 5 %
5100-300 mMammonium acetate1drop
65 %MPD1reservoirot 10 %
750 mMsodium cacodylate1reservoir
81
91

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 22, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 5429 / % possible obs: 95.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 44.6
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 8.05 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / % possible obs: 95.4 % / Redundancy: 4.9 % / Num. measured all: 26632
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 8.05

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HELIX 1 OF THE RNA DODECAMER CONTAINING THE E. COLI SHINE DALGARNO SEQUENCE (NDB ID ARL062) WITH THE SEQUENCE MUTATED TO R(GGCGCUUGCGUC).

Resolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.24 -0.1 %
Rwork0.191 --
obs0.191 5142 -
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 0 158 1166
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.26
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å /
RfactorNum. reflection
Rfree0.41 -
Rwork0.36 458
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1BERMANBERMAN
X-RAY DIFFRACTION2BERMANBERMAN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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