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- PDB-2hc7: 2'-selenium-T A-DNA [G(TSe)GTACAC] -

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Basic information

Entry
Database: PDB / ID: 2hc7
Title2'-selenium-T A-DNA [G(TSe)GTACAC]
Components5'-D(*GP*(2ST)P*GP*TP*AP*CP*AP*C)-3'
KeywordsDNA / SE-DNA / 2'-SE-T-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJiang, J. / Sheng, J. / Huang, Z.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of 2'-Selenium modified T A-DNA G(TSe)GTACAC
Authors: Jiang, J. / Sheng, J. / Huang, Z.
History
DepositionJun 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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*(2ST)P*GP*TP*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,5201
Polymers2,5201
Non-polymers00
Water77543
1
A: 5'-D(*GP*(2ST)P*GP*TP*AP*CP*AP*C)-3'

A: 5'-D(*GP*(2ST)P*GP*TP*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,0392
Polymers5,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)42.221, 42.221, 24.026
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*(2ST)P*GP*TP*AP*CP*AP*C)-3'


Mass: 2519.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS VIA PHOSPHORAMIDITE
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% MPD, 40 mM Na Cacodylate, 12 mM Sperimine tetra-HCI, 80 mM Sodium Chloride and 20 mM Magnesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Na Cacodylate11
3Sperimine tetra-HCI11
4Sodium Chloride11
5Magnesium Chloride11
6H2O11
7MPD12
8Na Cacodylate12
9Sodium Chloride12
10Magnesium Chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 4577 / Num. obs: 4577 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 10 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Z7I

1z7i


Resolution: 1.4→18.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 711051.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: DNA-RNA
RfactorNum. reflection% reflectionSelection details
Rfree0.187 435 10.2 %RANDOM
Rwork0.17 ---
all0.172 4252 --
obs0.17 4252 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0525 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.4→18.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 43 206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d34.3
X-RAY DIFFRACTIONc_improper_angle_d2.04
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 52 9.6 %
Rwork0.221 492 -
obs-492 73.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_ums.parion.top
X-RAY DIFFRACTION5cac.parums.top

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