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- PDB-1d7z: CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A... -

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Basic information

Entry
Database: PDB / ID: 1d7z
TitleCRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A RESOLUTION
Components5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'
KeywordsDNA / HEXITOL NUCLEIC ACID / DNA ANALOGUE / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.21 Å
AuthorsDeclercq, R. / Van Meervelt, L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Crystal structure of double helical hexitol nucleic acids.
Authors: Declercq, R. / Van Aerschot, A. / Read, R.J. / Herdewijn, P. / Van Meervelt, L.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1995
Title: 1',5'-Anhydrohexitol nucleic acids, a new promising antisense construct
Authors: Van Aerschot, A. / Verheggen, I. / Hendrix, C. / Herdewijn, P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: 1',5'-anhydro-2',3'-dideoxy-2'-(guanin-9-yl)-D-arabino-hexitol
Authors: Declercq, R. / Herdewijn, P. / Van Meervelt, L.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Oligonucleotides with 1',5'-anhydrohexitol nucleoside building blocks: Crystallization and preliminary X-ray studies of H(GTGTACAC)
Authors: Declercq, R. / Van Aerschot, A. / Herdewijn, P. / Van Meervelt, L.
History
DepositionOct 21, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 28, 2002Provider: 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 / citation_author / database_2 / diffrn_source / struct_conn
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Theoretical massNumber of molelcules
Total (without water)2,5391
Polymers2,5391
Non-polymers00
Water68538
1
A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'

A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Theoretical massNumber of molelcules
Total (without water)5,0782
Polymers5,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Unit cell
Length a, b, c (Å)36.364, 36.364, 69.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Cell settinghexagonal
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-21-

HOH

21A-56-

HOH

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Components

#1: DNA chain 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Mass: 2538.831 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE MOLECULE WAS CHEMICALLY SYNTESISED (SEE REFERENCE 1)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CACODYLATE BUFFER, KCL, BACL2, SPERMINE TETRACHLORIDE AND MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE BUFFER11
2SPERMINE11
3KCL11
4BACL211
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.4 mMoligomer solution1drop
210 %(v/v)MPD1drop
312 mMspermine hydrochloride1drop
480 mM1dropK+
520 mM1dropBa+
640 mMcacodylate1droppH7.0
735 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. all: 1344 / Num. obs: 1344 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 16.8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 38.8
Reflection shellResolution: 2.21→2.25 Å / Rmerge(I) obs: 0.168 / % possible all: 74.1
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 74.1 % / Rmerge(I) obs: 0.168

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Processing

Software
NameClassification
GLRFphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.21→20 Å / Cross valid method: NONE USED / σ(F): 0 / σ(I): 0
Stereochemistry target values: BASES: TAYLOR AND KENNARD VALUES; THE REST: VALUES BASED ON SINGLE CRYSTAL STRUCTURE OF HNA BUILDING BLOCKS
RfactorNum. reflection% reflection
Rwork0.233 --
all0.233 1329 -
obs0.233 1329 83.8 %
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 169 0 38 207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.233 / Rfactor obs: 0.233 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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