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- PDB-238d: CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGG(BR)CATGCCT): COMPARISO... -

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Basic information

Entry
Database: PDB / ID: 238d
TitleCRYSTAL STRUCTURE OF THE DNA DECAMER D(AGG(BR)CATGCCT): COMPARISON WITH D(AGGCATGCCT) AND IMPLICATIONS FOR COBALT HEXAMMINE BINDING TO DNA
ComponentsDNA (5'-D(*AP*GP*GP*(CBR)P*AP*TP*GP*CP*CP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / FLIPPED-OUT BASES / BASE TRIPLET
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNunn, C.M.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1996
Title: Crystal structure of d(AGGBrCATGCCT): implications for cobalt hexammine binding to DNA
Authors: Nunn, C.M.
History
DepositionNov 2, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 30, 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_conn
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_conn.pdbx_leaving_atom_flag

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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*(CBR)P*AP*TP*GP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,1241
Polymers3,1241
Non-polymers00
Water1,00956
1
A: DNA (5'-D(*AP*GP*GP*(CBR)P*AP*TP*GP*CP*CP*T)-3')

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


Theoretical massNumber of molelcules
Total (without water)6,2482
Polymers6,2482
Non-polymers00
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)33.200, 33.200, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 3123.901 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
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
4NH4OH11
5[CO(NH3)6]CL311
6WATER11
7MPD12
8WATER12
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 %1drop0.005mlNH4OH
410 mMhexamminecobalt(III) trichloride1drop0.003ml
550 %MPD1drop0.002ml
650 %MPD1reservoir
71
81

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→9.5 Å / Num. obs: 1777 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.071
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 9.2 Å / Num. obs: 3487 / % possible obs: 96.9 % / Observed criterion σ(F): 0

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
RefinementResolution: 2→8 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rwork0.196 --
obs0.196 1748 -
Rfree--29.4
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 1 56 259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.027
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04

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