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- PDB-3fa1: Crystal Structure of Tellurium Derivatized DNA -

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Basic information

Entry
Database: PDB / ID: 3fa1
TitleCrystal Structure of Tellurium Derivatized DNA
Components5'-D(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3'
KeywordsDNA / Tellurium DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSheng, J. / Tatsuya, M. / Hassan, A.E. / Huang, Z.
CitationJournal: To be Published
Title: Crystal Structure of Tellurium Derivatized DNA
Authors: Sheng, J. / Tatsuya, M. / Hassan, A.E. / Huang, Z.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)2,6191
Polymers2,6191
Non-polymers00
Water50428
1
A: 5'-D(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3'

A: 5'-D(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)5,2382
Polymers5,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.695, 42.695, 24.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*DGP*(UMS)P*DGP*(TTI)P*DAP*DCP*DAP*DC)-3'


Mass: 2619.151 Da / Num. of mol.: 1 / Mutation: Tellurium modified deoxy-Uridine / Source method: obtained synthetically / Details: Tellurium contained DNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD,sodium cacodylate,spermine tetra-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium cacodylate11
3Spermine tetra-HCl1
4MPD12
5Sodium cacodylate12

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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: Apr 12, 2008
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→18.89 Å / Num. obs: 3659 / % possible obs: 94.4 % / Observed criterion σ(F): 50 / Observed criterion σ(I): 5 / Redundancy: 8.63 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.93 / Net I/σ(I): 14.9 / Scaling rejects: 239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.5-1.555.30.4272.414692770.4274.9
1.55-1.626.50.3113.521283270.4985.2
1.62-1.698.40.2245.130223590.5496.2
1.69-1.789.470.1766.635633760.5899.2
1.78-1.899.490.1957.636443830.799.7
1.89-2.049.360.1379.835463780.6898.7
2.04-2.249.430.1441135833780.8398.7
2.24-2.569.50.11113.236653840.8799.2
2.56-3.239.280.0732436423891.2597.5
3.23-18.898.370.05254.235584082.4393.6

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Processing

Software
NameVersionClassificationNB
d*TREK9.9BNLDzdata processing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
d*TREKdata scaling
CNSphasing
RefinementStarting model: 1DNS

1dns


Resolution: 1.5→18.89 Å / Occupancy max: 1 / Occupancy min: 0.35 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE BIJVOET PAIRS WERE USED IN PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.215 691 10.1 %Random
Rwork0.193 ---
all0.1947 ---
obs0.1947 783 93.8 %-
Solvent computationBsol: 54.275 Å2
Displacement parametersBiso max: 47.55 Å2 / Biso mean: 22.409 Å2 / Biso min: 14.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.602 Å20 Å20 Å2
2---0.602 Å20 Å2
3---1.204 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 0 28 190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.694
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.5452
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.1152.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2dna-rna_rep_jia.paramdna-rna_jia.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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