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- PDB-1i9x: CRYSTAL STRUCTURE OF BPS-U2 SNRNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 1i9x
TitleCRYSTAL STRUCTURE OF BPS-U2 SNRNA DUPLEX
Components5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3'
KeywordsRNA / pre-mRNA splicing / bulged adenosine / three helix junction
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.18 Å
AuthorsBerglund, J.A. / Rosbash, M. / Schultz, S.C.
CitationJournal: RNA / Year: 2001
Title: Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines.
Authors: Berglund, J.A. / Rosbash, M. / Schultz, S.C.
History
DepositionMar 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3'
B: 5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3'


Theoretical massNumber of molelcules
Total (without water)8,2532
Polymers8,2532
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.75, 42.40, 33.14
Angle α, β, γ (deg.)90.00, 92.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 4126.509 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The UACUAAC is the conserved branchpoint sequence in budding yeast and the GUAGUA is conserved in the U2 snRNP particle.
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, Spermine, Glycerol, tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Temp details: 303.0 then shifted to 287.0
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Spermine11
3Glycerol11
4tris11
5MPD12
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-5 mg/mlRNA1drop
210 %MPD1reservoir
310-25 %glycerol1reservoir
425 mMTris1reservoir
51-3 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 10, 1999 / Details: Yale mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 4369 / Num. obs: 4125 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 4.7 / Net I/σ(I): 30.1
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.6 / Num. unique all: 440 / Rsym value: 27.7 / % possible all: 94
Reflection
*PLUS
Num. measured all: 20240
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.18→8 Å / Isotropic thermal model: Anistropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
Details: Bulk solvent was not used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 410 -Random
Rwork0.253 ---
all-4145 --
obs-3980 96 %-
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1-22.18 Å20 Å212.48 Å2
2---15.43 Å20 Å2
3----6.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.18→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 546 0 22 568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d12.7
X-RAY DIFFRACTIONc_improper_angle_d1.49
LS refinement shellResolution: 2.18→2.31 Å / Rfactor Rfree error: 0.055
RfactorNum. reflection% reflection
Rfree0.457 69 -
Rwork0.427 --
obs--93.2 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg12.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49
LS refinement shell
*PLUS
Rfactor Rfree: 0.457 / Rfactor Rwork: 0.427

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