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- PDB-4f4n: Crystal structure of 2-se-thymidine derivatized dna 8mer -

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Basic information

Entry
Database: PDB / ID: 4f4n
TitleCrystal structure of 2-se-thymidine derivatized dna 8mer
Components5'-D(*GP*TP*GP*(US3)P*AP*CP*AP*C)-3'
KeywordsDNA / 2-SE-THYMIDINE DNA / Structural Genomics
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhang, W. / Sheng, J. / Huang, Z.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of 2-se-thymidine derivatized dna 8mer
Authors: Zhang, W. / Sheng, J. / Huang, Z.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*TP*GP*(US3)P*AP*CP*AP*C)-3'
C: 5'-D(*GP*TP*GP*(US3)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,9792
Polymers4,9792
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint8 kcal/mol
Surface area2780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.635, 44.635, 41.305
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain 5'-D(*GP*TP*GP*(US3)P*AP*CP*AP*C)-3'


Mass: 2489.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE 2-SE-THYMIDINE RESIDUE WAS CHEMICALLY SYNTHESIZED AND INCORPORATED INTO DNA OLIGONUCLEOTIDE THROUGH SOLID PHASE SYNTHESIS
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.82 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→18.22 Å / Num. all: 193605 / Num. obs: 10889

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→18.22 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18111 514 4.7 %RANDOM
Rwork0.15416 ---
obs0.15543 10318 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 74 396
LS refinement shellResolution: 1.302→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 26 -
Rwork0.285 476 -
obs--59.98 %

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