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- PDB-1d87: CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL... -

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Basic information

Entry
Database: PDB / ID: 1d87
TitleCONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES
ComponentsDNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / DNA-RNA HYBRID COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsEgli, M. / Usman, N. / Rich, A.
Citation
Journal: Biochemistry / Year: 1993
Title: Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes.
Authors: Egli, M. / Usman, N. / Rich, A.
#1: Journal: Nucleic Acids Res. / Year: 1992
Title: Large Scale Chemical Synthesis, Purification and Crystallization of RNA-DNA Chimeras
Authors: Usman, N. / Egli, M. / Rich, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal Structure of an Okazaki Fragment at 2 Angstroms Resolution
Authors: Egli, M. / Usman, N. / Zhang, S. / Rich, A.
History
DepositionAug 28, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1222
Polymers6,1222
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.500, 44.230, 44.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')


Mass: 3061.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Details: Egli, M., (1992) Proc.Nat.Acad.Sci.USA, 89, 534.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 mMoligonucleotide1dropsingle strand concentration
230 mMsodium cacodylate1drop
37.5 mMmagnesium chloride1drop
47.5 mMspermine tetrachloride1drop
540 %(v/v)MPD1reservoir
61

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 1592 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2.25 Å / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementHighest resolution: 2.25 Å / σ(F): 2 /
RfactorNum. reflection
obs0.178 1592
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 406 0 110 516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.14
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.178 / Highest resolution: 2.25 Å / Num. reflection obs: 1592 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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