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- PDB-3hgd: Crystal Structure of 2-Se-Thymidine Derivatized DNA -

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Basic information

Entry
Database: PDB / ID: 3hgd
TitleCrystal Structure of 2-Se-Thymidine Derivatized DNA
Components5'-D(*GP*(UMS)P*GP*(US3)P*AP*CP*AP*C)-3'
KeywordsDNA / 2-Se-thymidine DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsSheng, J. / Hassan, A.E. / Zhang, W. / Huang, Z.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: High fidelity of base pairing by 2-selenothymidine in DNA.
Authors: Hassan, A.E. / Sheng, J. / Zhang, W. / Huang, Z.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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*(UMS)P*GP*(US3)P*AP*CP*AP*C)-3'
B: 5'-D(*GP*(UMS)P*GP*(US3)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1372
Polymers5,1372
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint6 kcal/mol
Surface area2850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.828, 45.828, 42.501
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*(UMS)P*GP*(US3)P*AP*CP*AP*C)-3'


Mass: 2568.538 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: MPD,sodium cacodylate,spermine tetra-HCl, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC Q210 / Detector: CCD / Date: Dec 7, 2008
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 6839 / % possible obs: 95.1 % / Redundancy: 17 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.159
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.57-1.646.60.60774.9
1.64-1.78.70.41985.3
1.7-1.7811.10.27196.3
1.78-1.8715.50.229100
1.87-1.9921.40.192100
1.99-2.1421.70.161100
2.14-2.3621.70.142100
2.36-2.721.70.118100
2.7-3.420.90.08899.6
3.4-5016.80.07194.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→50 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.22 725 10.1 %
Rwork0.204 --
obs0.204 6688 93.3 %
Solvent computationBsol: 56.701 Å2
Displacement parametersBiso mean: 27.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.292 Å20 Å2
2--0.09 Å20 Å2
3----0.179 Å2
Refinement stepCycle: LAST / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 0 35 359
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
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_deg
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_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.5672
X-RAY DIFFRACTIONc_scangle_it2.2662.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep_jia.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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