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- PDB-123d: DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODEL... -

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Basic information

Entry
Database: PDB / ID: 123d
TitleDNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsHahn, M. / Heinemann, U.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.
Authors: Hahn, M. / Heinemann, U.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: C-C-A-G-G-C-M5C-T-G-G: Helical Fine Structure, Hydration, and Comparison with C-C-A-G-G-C-C-T-G-G
Authors: Heinemann, U. / Hahn, M.
#2: Journal: Embo J. / Year: 1992
Title: Double Helix Conformation, Groove Dimensions and Ligand Binding Potential of a G/C-Stretch in B-DNA
Authors: Heinemann, U. / Alings, C. / Bansal, M.
#3: Journal: Embo J. / Year: 1991
Title: The Conformation of a B-DNA Decamer Is Mainly Determined by Its Sequence and Not by Crystal Environment
Authors: Heinemann, U. / Alings, C.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Study of One Turn of G/C-Rich B-DNA
Authors: Heinemann, U. / Alings, C.
History
DepositionMay 3, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1202
Polymers6,1202
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.770, 53.770, 34.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11B-98-

HOH

21B-99-

HOH

31B-100-

HOH

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Components

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


Mass: 3060.020 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5 / Details: pH 7.50, MICRODIALYSIS, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4WATER12
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Details: Heinemann, U., (1991) Embo J., 10, 35.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMDNA solution1
220 mMsodium cacodylate1
350 mMmagnesium chloride1
440 %MPD1
520 mMsodium cacodylate1
650 mMmagnesium chloride12

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. all: 7209 / Num. obs: 4704
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.7→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 3799
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 80 486
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. reflection obs: 3799 / σ(F): 2 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.111
X-RAY DIFFRACTIONx_angle_d0.068
X-RAY DIFFRACTIONx_plane_restr0.083
X-RAY DIFFRACTIONx_chiral_restr0.172
X-RAY DIFFRACTIONx_mcbond_it3.92
X-RAY DIFFRACTIONx_mcangle_it5.15

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