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- PDB-1d89: A DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNI... -

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Basic information

Entry
Database: PDB / ID: 1d89
TitleA DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNIQUE LATTICE AND EXHIBITS A NEW BEND
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDiGabriele, A.D. / Steitz, T.A.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend.
Authors: DiGabriele, A.D. / Steitz, T.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Crystal Lattice Packing Is Important in Determining the Bend of a DNA Dodecamer Containing an Adenine Tract
Authors: DiGabriele, A.D. / Sanderson, M.R. / Steitz, T.A.
History
DepositionJul 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,9746
Polymers21,9746
Non-polymers00
Water99155
1
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.780, 66.050, 42.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-121-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3')


Mass: 3689.446 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Mass: 3635.362 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 283.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlduplex1drop
293 mM1reservoirMgCl2
310 mMsodium cacodylate1reservoir
41 mMspermine tetrahydrochloride1reservoir
531 %MPD1reservoir
61
71

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Data collection

DiffractionMean temperature: 263 K
DetectorType: UCSD MARK II / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 5545
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 92 % / Rmerge(I) obs: 0.051 / Num. measured all: 24066

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.3→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.232 -
obs0.232 4595
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1458 0 55 1513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. reflection obs: 4595 / σ(F): 2 / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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