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- PDB-3ijk: 5-OMe modified DNA 8mer -

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Basic information

Entry
Database: PDB / ID: 3ijk
Title5-OMe modified DNA 8mer
Components5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'
KeywordsDNA / selenium / 5-methoxy-uridine
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsSheng, J. / Zhang, W. / Hassan, A.E.A. / Gan, J. / Huang, Z.
CitationJournal: Chemistryselect / Year: 2023
Title: Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate
Authors: Fang, Z. / Dantsu, Y. / Chen, C. / Zhang, W. / Huang, Z.
History
DepositionAug 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_entity_src_syn / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,5221
Polymers2,5221
Non-polymers00
Water54030
1
A: 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'

A: 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,0432
Polymers5,0432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1940 Å2
ΔGint8 kcal/mol
Surface area2910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 43.210, 23.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'


Mass: 2521.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5-OMe modified DNA octamer / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v / v MPD, 40 mM Na Cacodylate pH 6.0, 12 mM Spermine tetra-HCl, 80 mM Strontium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 10495 / Num. obs: 5561 / % possible obs: 94.5 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.35
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1 / Num. unique all: 264 / % possible all: 50.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: 1DNS

1dns


Resolution: 1.3→30.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.656 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21884 256 4.6 %RANDOM
Rwork0.19672 ---
all0.19769 5574 --
obs-5301 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.795 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.056 Å0.055 Å
Refinement stepCycle: LAST / Resolution: 1.3→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 30 193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021180
X-RAY DIFFRACTIONr_angle_refined_deg1.63270
X-RAY DIFFRACTIONr_chiral_restr0.0680.231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0283
X-RAY DIFFRACTIONr_nbd_refined0.360.269
X-RAY DIFFRACTIONr_nbtor_refined0.2820.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.211
X-RAY DIFFRACTIONr_scbond_it0.8323259
X-RAY DIFFRACTIONr_scangle_it1.2724.5270
LS refinement shellResolution: 1.303→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 6 -
Rwork0.47 249 -
obs--62.04 %
Refinement TLS params.Method: refined / Origin x: 11.4162 Å / Origin y: 12.7391 Å / Origin z: 2.3922 Å
111213212223313233
T0.0418 Å20.0001 Å2-0.0099 Å2-0.0201 Å2-0.0003 Å2--0.025 Å2
L0.7644 °2-0.9107 °2-0.0164 °2-2.6011 °2-0.3799 °2--0.1056 °2
S-0.0447 Å °-0.014 Å °-0.0434 Å °0.2121 Å °0.0378 Å °-0.0153 Å °0.003 Å °0.0553 Å °0.0068 Å °

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