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- PDB-2gun: RNA-Binding Affinities and Crystal Structure of Oligonucleotides ... -

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Basic information

Entry
Database: PDB / ID: 2gun
TitleRNA-Binding Affinities and Crystal Structure of Oligonucleotides containing Five-Atom Amide-Based Backbone Structures
Components
  • 5'-D(*TP*TP*CP*(T2T)P*(CBR)P*TP*TP*C)-3'
  • 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'
KeywordsDNA/RNA / DNA:RNA hybrid / amide bearing DNA / thymidine dimers / internucleosidic amide linkage / DNA / RNA / DNA-RNA COMPLEX
Function / homologyCOBALT (III) ION / SPERMINE / DNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Biochemistry / Year: 2006
Title: RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures.
Authors: Pallan, P.S. / von Matt, P. / Wilds, C.J. / Altmann, K.-H. / Egli, M.
History
DepositionMay 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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_site
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_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

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Assembly

Deposited unit
A: 5'-D(*TP*TP*CP*(T2T)P*(CBR)P*TP*TP*C)-3'
B: 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0325
Polymers5,7122
Non-polymers3203
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.231, 47.231, 24.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: DNA chain 5'-D(*TP*TP*CP*(T2T)P*(CBR)P*TP*TP*C)-3'


Mass: 2745.793 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'


Mass: 2965.895 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5 mM cobalt hexamine, 5 mM spermine tetrachloride, 80 mM sodium cacodylate buffer (pH = 7.0) and 10% (v/v) 2-methyl-2,4-pentanediol (MPD)., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1cobalt hexamine11
2spermine tetrachloride11
3sodium cacodylate11
4MPD11
5H2O11
6cobalt hexamine12
7sodium cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9203 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2001
RadiationMonochromator: Si Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9203 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 2602 / Num. obs: 2391 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.057
Reflection shellHighest resolution: 2.8 Å / % possible all: 92.3

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 4
Stereochemistry target values: L. Clowney et.al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases J. Am. Chem. Soc., (1996) 118, 509-518; A. Gelbin et.al., Geometric Parameters in Nucleic ...Stereochemistry target values: L. Clowney et.al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases J. Am. Chem. Soc., (1996) 118, 509-518; A. Gelbin et.al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents J. Am. Chem. Soc., (1996) 118, 519-529. G. Parkinson et. al., New parameters for the refinement of nucleic acid-containing structures Acta Cryst. (1996). D52, 57-64.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 215 -Random
Rwork0.235 ---
all-2586 --
obs-2388 92.3 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 399 19 17 435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.3

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