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- PDB-1d13: MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT) -

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Basic information

Entry
Database: PDB / ID: 1d13
TitleMOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)
ComponentsDNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFrederick, C.A. / Quigley, G.J. / Teng, M.-K. / Coll, M. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J.
CitationJournal: Eur.J.Biochem. / Year: 1989
Title: Molecular structure of an A-DNA decamer d(ACCGGCCGGT).
Authors: Frederick, C.A. / Quigley, G.J. / Teng, M.K. / Coll, M. / Van der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.
History
DepositionOct 20, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water64936
1
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')

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


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
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)39.230, 39.230, 78.010
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*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA decamer1dropsingle strand
240 mMsodium cacodylate1drop
313.0 mMmagnesium chloride1drop
45.0 mMspermine tetrachloride1drop
55 %MPD1drop
650 %MPD1reservoir

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Data collection

DiffractionMean temperature: 283 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 4200 / Num. obs: 1434 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→20 Å / σ(F): 2 /
RfactorNum. reflection
obs0.18 1434
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 36 238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.026
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 1434 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.026

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