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- PDB-1ik5: Crystal Structure of a 14mer RNA Containing Double UU Bulges in T... -

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Basic information

Entry
Database: PDB / ID: 1ik5
TitleCrystal Structure of a 14mer RNA Containing Double UU Bulges in Two Crystal Forms: A Novel U*(AU) Intramolecular Base Triple
Components
  • 5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3'
  • 5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3'
KeywordsRNA / RNA duplex / UU-bulges / base triple / kink
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDeng, J. / Xiong, Y. / Sudarsanakumar, C. / Shi, K. / Sundaralingam, M.
CitationJournal: RNA / Year: 2001
Title: Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.
Authors: Deng, J. / Xiong, Y. / Sudarsanakumar, C. / Shi, K. / Sundaralingam, M.
History
DepositionMay 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3'
B: 5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0574
Polymers9,0082
Non-polymers492
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.04, 29.53, 52.44
Angle α, β, γ (deg.)90, 120.83, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 4503.547 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: potential hair pin fragment with highly conserved UUCG loop
#2: RNA chain 5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3'


Mass: 4504.531 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: cacodylate, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2MgCl211
3MPD11
4MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMRNA1dropdouble strand
210 mMspermine tetrahydrochloride1drop
340 mMsodium cacodylate1drop
410 %(v/v)1drop
520 mM1dropMgCl2
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 2, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 7100 / % possible obs: 91 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.232 683
Rwork0.209 -
all-7463
obs-6948
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 584 4 67 655
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0084
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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