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- PDB-1i2x: 2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM -

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Basic information

Entry
Database: PDB / ID: 1i2x
Title2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM
ComponentsDNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
KeywordsDNA-RNA HYBRID / 'adenine bulge / A-type NA / DNA/RNA hybrid'
Function / homologySPERMIDINE / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTereshko, V. / Wallace, S. / Usman, N. / Wincott, F. / Egli, M.
CitationJournal: RNA / Year: 2001
Title: X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
Authors: Tereshko, V. / Wallace, S.T. / Usman, N. / Wincott, F.E. / Egli, M.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
B: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
D: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
C: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0305
Polymers13,8854
Non-polymers1451
Water1,42379
1
A: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
B: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)6,9422
Polymers6,9422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
C: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0883
Polymers6,9422
Non-polymers1451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.69, 47.71, 113.62
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid
DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')


Mass: 3471.194 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: spermidine, MPD. pH 6.0, VAPOR DIFFUSION, SITTING DROP at 298
Components of the solutions
IDNameCrystal-IDSol-ID
1spermidine11
2MPD11
3MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.72 mMDNA1drop
220 mMsodium cacodylate1reservoir
325 mMspermine1reservoir
440 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 26, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 6220 / Num. obs: 6220 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 6180 / % possible obs: 94.6 % / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 453 7.3 %random
Rwork0.2495 ---
all-6220 --
obs-6220 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 920 10 81 1011
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.03
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
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.358 / Rfactor Rwork: 0.332 / Num. reflection Rwork: 594

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