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- PDB-232d: THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT) -

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Basic information

Entry
Database: PDB / ID: 232d
TitleTHE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)
ComponentsDNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / FLIPPED-OUT BASES
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsNunn, C.M. / Neidle, S.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The high resolution crystal structure of the DNA decamer d(AGGCATGCCT).
Authors: Nunn, C.M. / Neidle, S.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Structure of Chain-linked DNA as a Possible Model for the Transcription Bubble
Authors: Nunn, C.M. / Neidle, S.
History
DepositionSep 5, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 22, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3673
Polymers3,0451
Non-polymers3222
Water1,36976
1
A: DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7346
Polymers6,0902
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)32.700, 32.700, 78.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-16-

HOH

21A-41-

HOH

31A-76-

HOH

41A-77-

HOH

51A-85-

HOH

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Components

#1: DNA chain DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.91 Å3/Da / Density % sol: 35.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 287.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4[CO(NH3)6]CL311
5NH4OH11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 287 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mMDNA1drop0.005ml in 30 mM sodium cacodylate
230 mMsodium cacodylate1drop
335 %(w/v)1drop0.005mlNH4OH
410 mMhexammine-pentanediol1drop0.003ml
550 %(v/v)MPD1drop0.002ml
650 %(v/v)MPD1reservoir
71

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.3 Å / Num. obs: 6494 / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 19.2 Å / % possible obs: 98.2 %
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.32 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
SHELXL-93refinement
DENZOdata reduction
RefinementResolution: 1.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.216 --
obs0.1385 6494 98.2 %
all-6494 -
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 14 76 292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_deg1.5
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg1.8

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