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- PDB-1d9h: Structural origins of the exonuclease resistance of a zwitterionic RNA -

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Basic information

Entry
Database: PDB / ID: 1d9h
TitleStructural origins of the exonuclease resistance of a zwitterionic RNA
ComponentsDNA/RNA (5'-D(*GP*CP*GP*TP*AP)-R(*(U31)P)-D(*AP*CP*GP*C)-3')
KeywordsDNA / RNA / EXONUCLEASE RESISTANCE / A-DNA
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsTeplova, M. / Wallace, S.T. / Tereshko, V. / Minasov, G. / Simons, A.M. / Cook, P.D. / Manoharan, M. / Egli, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural origins of the exonuclease resistance of a zwitterionic RNA
Authors: Teplova, M. / Wallace, S.T. / Tereshko, V. / Minasov, G. / Symons, A.M. / Cook, P.D. / Manoharan, M. / Egli, M.
History
DepositionOct 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Jan 3, 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_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*GP*CP*GP*TP*AP)-R(*(U31)P)-D(*AP*CP*GP*C)-3')
B: DNA/RNA (5'-D(*GP*CP*GP*TP*AP)-R(*(U31)P)-D(*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2082
Polymers6,2082
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.17, 42.77, 45.18
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*GP*CP*GP*TP*AP)-R(*(U31)P)-D(*AP*CP*GP*C)-3')


Mass: 3104.073 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, POTASSIUN CACODYLATE, KCL, SPERMINE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1POTASSIUN CACODYLATE11
2KCL11
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMprotein1drop
240 mMpotassium cacodylate1drop
380 mM1dropKCl
412 mMspermine1drop
510 %(v/v)1drop
635 %MPD1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 6444 / Num. obs: 6444 / % possible obs: 94.8 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 1.6 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementResolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.243 -RANDOM
Rwork0.187 --
obs0.187 6234 -
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 458 8 435 901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.07
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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