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- PDB-2bj6: Crystal Structure of a decameric HNA-RNA hybrid -

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Basic information

Entry
Database: PDB / ID: 2bj6
TitleCrystal Structure of a decameric HNA-RNA hybrid
Components
  • 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
  • SYNTHETIC HNA
KeywordsNUCLEIC ACID (HNA/RNA) / DNA / RNA / HNA / HEXITOL NUCLEIC ACID / HYBRID / DUPLEX / MODIFIED NUCLEIC ACID / ANTISENSE / BACKBONE MODIFICATION / NUCLEIC ACID (HNA-RNA) complex
Function / homologyDNA / RNA
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMaier, T. / Przylas, I. / Straeter, N. / Herdewijn, P. / Saenger, W.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Reinforced Hna Backbone Hydration in the Crystal Structure of a Decameric Hna/RNA Hybrid
Authors: Maier, T. / Przylas, I. / Strater, N. / Herdewijn, P. / Saenger, W.
#1: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Molecular Dynamics Simulation to Inverstigate Differences in Minor Groove Hydration of Hna-RNA Hybrids as Compared to Hna-DNA Complexes
Authors: Dewinter, H. / Lescrinier, E. / Vanaerschot, A. / Herdewijn, P.
#2: Journal: Chem.Biol. / Year: 2000
Title: Solution Structure of a Hna-RNA Hybrid
Authors: Lescrinier, E. / Esnouf, R. / Schraml, J. / Busson, R. / Heus, H.A. / Hilbers, C.W. / Herdewijn, P.
#3: Journal: J.Am.Chem.Soc. / Year: 2002
Title: Crystal Structure of Double Helical Hexitol Nucleic Acids
Authors: Declercq, R. / Vanaerschot, A. / Read, R.J. / Herdewijn, P. / Vanmeervelt, L.
#4: Journal: Acta Crystallogr.,Sect.C / Year: 1996
Title: 1,5-Anhydro-2,3-Dideoxy-2-(Guanin-9-Yl)-D-Arabino-Hexitol
Authors: Declerq, R. / Herdewijn, P. / Vanmeervelt, L.
History
DepositionJan 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: SYNTHETIC HNA
B: SYNTHETIC HNA
C: SYNTHETIC HNA
D: SYNTHETIC HNA
E: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
F: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
G: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
H: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,92913
Polymers25,4498
Non-polymers4805
Water2,936163
1
A: SYNTHETIC HNA
E: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4583
Polymers6,3622
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SYNTHETIC HNA
F: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4583
Polymers6,3622
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SYNTHETIC HNA
G: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6505
Polymers6,3622
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: SYNTHETIC HNA
H: 5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)6,3622
Polymers6,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.910, 113.910, 55.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain
SYNTHETIC HNA


Mass: 3145.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS, PHOSPHOROTHIOATE / Source: (synth.) HOMO SAPIENS (human)
#2: RNA chain
5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'


Mass: 3216.973 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS, PHOSPHOROTHIOATE / Source: (synth.) HOMO SAPIENS (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.53 Å3/Da / Density % sol: 66.2 %
Crystal growDetails: 0.9M LISO4, 10MM MG(AC)2,0.1M TRIS/HCL, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.92067
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92067 Å / Relative weight: 1
ReflectionResolution: 2.54→35 Å / Num. obs: 11676 / % possible obs: 99.4 % / Redundancy: 6.64 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.7
Reflection shellResolution: 2.54→2.63 Å / Mean I/σ(I) obs: 3.2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→35 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DIFFERENT ATOM NUMBERING SCHEMES ARE USED IN THE LITERATURE. PLEASE SEE PRIMARY AND SECONDARY CITATIONS FOR A DETAILED DESCRIPTION. STEREOCHEMICAL PARAMETERS FOR HNA MONOMERS HAVE BEEN ...Details: DIFFERENT ATOM NUMBERING SCHEMES ARE USED IN THE LITERATURE. PLEASE SEE PRIMARY AND SECONDARY CITATIONS FOR A DETAILED DESCRIPTION. STEREOCHEMICAL PARAMETERS FOR HNA MONOMERS HAVE BEEN DERIVED FROM SMALL MOLECULE X-RAY STRUCTURES, SEE SECONDARY REFERENCES
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10.2 %RANDOM
Rwork0.217 ---
obs0.217 11676 99.8 %-
Displacement parametersBiso mean: 48.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1688 25 163 1876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.245
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.64 Å / Total num. of bins used: 23 /
RfactorNum. reflection
Rfree0.4695 54
Rwork0.4692 455

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