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- PDB-1sdr: CRYSTAL STRUCTURE OF AN RNA DODECAMER CONTAINING THE ESCHERICHIA ... -

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Basic information

Entry
Database: PDB / ID: 1sdr
TitleCRYSTAL STRUCTURE OF AN RNA DODECAMER CONTAINING THE ESCHERICHIA COLI SHINE-DALGARNO SEQUENCE
Components
  • RNA (5'-R(*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3')
  • RNA (5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSchindelin, H. / Zhang, M. / Bald, R. / Fuerste, J.-P. / Erdmann, V.A. / Heinemann, U.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence.
Authors: Schindelin, H. / Zhang, M. / Bald, R. / Furste, J.P. / Erdmann, V.A. / Heinemann, U.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: A Single Base Change in the Shine-Dalgarno Region of 16s RRNA of Escherichia Coli Affects Translation of Many Proteins
Authors: Jacobs, W.F. / Santer, M. / Dahlberg, A.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Specialized Ribosome Systems: Preferential Translation of a Single MRNA Species by a Subpopulation of Mutated Ribosomes in Escherichia Coli
Authors: Hui, A. / De Boer, H.A.
History
DepositionDec 11, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,2194
Polymers15,2194
Non-polymers00
Water70339
1
A: RNA (5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)-3')
B: RNA (5'-R(*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,6102
Polymers7,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)-3')
D: RNA (5'-R(*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,6102
Polymers7,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.690, 30.900, 41.980
Angle α, β, γ (deg.)90.92, 103.63, 113.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.72859, -0.12371, -0.67368), (0.09391, -0.95622, 0.27717), (-0.67848, -0.26521, -0.68508)
Vector: 9.00667, -8.99483, 17.76623)

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Components

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


Mass: 3916.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3')


Mass: 3693.232 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.9 %
Crystal grow
*PLUS
Temperature: 32 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlRNA1drop
25 %(v/v)MPD1drop
3200 mM1dropMgCl2
530 %MPD1reservoir
6400 mM1reservoirMgCl2
740 mMsodium cacodylate1reservoir
4sodium cacodylate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 3050 / % possible obs: 83.6 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % possible obs: 83.6 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / % possible obs: 81.2 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 2957
Displacement parametersBiso mean: 13.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1006 0 39 1045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.82
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.73
X-RAY DIFFRACTIONx_plane_restr0.006

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