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- PDB-3bm0: Structure of DNA Octamer G(dUSe)G(5-SedU)ACAC -

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Basic information

Entry
Database: PDB / ID: 3bm0
TitleStructure of DNA Octamer G(dUSe)G(5-SedU)ACAC
Components5'-D(*GP*(2'-Se-U)P*GP*(5-Se-U)P*AP*CP*AP*C)-3'
KeywordsDNA / Selenium modified DNA/RNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJiang, J. / SHeng, J. / Hassan, A.E. / Huang, Z.
CitationJournal: Org.Lett. / Year: 2009
Title: Synthesis and crystallographic analysis of 5-Se-thymidine DNAs.
Authors: Hassan, A.E. / Sheng, J. / Jiang, J. / Zhang, W. / Huang, Z.
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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*(2'-Se-U)P*GP*(5-Se-U)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,5851
Polymers2,5851
Non-polymers00
Water50428
1
A: 5'-D(*GP*(2'-Se-U)P*GP*(5-Se-U)P*AP*CP*AP*C)-3'

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


Theoretical massNumber of molelcules
Total (without water)5,1692
Polymers5,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area1930 Å2
ΔGint7 kcal/mol
Surface area2910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.087, 42.087, 23.772
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*(2'-Se-U)P*GP*(5-Se-U)P*AP*CP*AP*C)-3'


Mass: 2584.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% V/V MPD, 40 MM SODIUM CACODYLATE (PH 7.0), 12 MM SPERMINE TETRA-HCL, 80 MM SODIUM CHLORIDE., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2SODIUM CACODYLATE11
3SPERMINE TETRA-HCL11
4NaClSodium chloride11
5MPD12
6SODIUM CACODYLATE12
7SPERMINE TETRA-HCL12
8NaClSodium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9797, 1.100, 0.9400
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.11
30.941
ReflectionResolution: 1.8→40 Å / Num. all: 2198 / Num. obs: 2087 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 10 / Num. unique all: 209 / % possible all: 95

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→15.76 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 692659.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 98 5.1 %RANDOM
Rwork0.21 ---
all0.22 ---
obs0.211 1922 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2936 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2---1.92 Å20 Å2
3---3.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→15.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 28 191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d28.9
X-RAY DIFFRACTIONc_improper_angle_d2.31
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 11 4 %
Rwork0.214 261 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_ums.pardna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5ums.top

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