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- PDB-1d62: THE STRUCTURE OF A /B-DNA$ DECAMER WITH AN I(SLASH)*A MISMATCH AN... -

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Entry
Database: PDB / ID: 1d62
TitleTHE STRUCTURE OF A /B-DNA$ DECAMER WITH AN I(SLASH)*A MISMATCH AND COMPARISON WITH THE G(SLASH)*A MISMATCH
Components5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3'
KeywordsDNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLipanov, A. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA.
Authors: Lipanov, A.A. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: The Structure of the /B-DNA Decamer / C-C-A-A-C-G-T-T-G-G and Comparison with the Isomorphous Decamers /C-C-A-A-G-A-T-T-G-G and /C-C-A-G-G-C-C-T-G-G
Authors: Prive, G.G. / Yanagi, K. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Study of One Turn of G(Slash)C-Rich B-/DNA
Authors: Heinemann, U. / Alings, C.
#3: Journal: Science / Year: 1987
Title: Helix Geometry, Hydration, and G(Dot)A Mismatch in a B-/DNA Decamer
Authors: Prive, G.G. / Heinemann, U. / Chandrasegaran, S. / Kan, L.-S. / Kopka, M.L. / Dickerson, R.E.
History
DepositionMar 1, 1992Deposition site: NDB / 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: Advisory / Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_special_symmetry / pdbx_validate_rmsd_angle
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_site.occupancy / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,0541
Polymers3,0541
Non-polymers00
Water90150
1
A: 5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3'

A: 5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,1082
Polymers6,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)32.210, 25.140, 34.140
Angle α, β, γ (deg.)90.00, 114.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-13-

HOH

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Components

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


Mass: 3054.016 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.53 mMDNA decamer1dropdouble helix
221.7 mMcalcium acetate1drop
321.7 mMsodium cacodylate1droppH7.0
40.43 mMspermidine1drop
59 %MPD1drop
640 %MPD1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.134 1195
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 203 0 50 253
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 1195 / Rfactor obs: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_angle_deg
X-RAY DIFFRACTIONn_dihedral_angle_d
X-RAY DIFFRACTIONn_improper_angle_d
X-RAY DIFFRACTIONn_mcbond_it
X-RAY DIFFRACTIONn_scbond_it
X-RAY DIFFRACTIONn_mcangle_it
X-RAY DIFFRACTIONn_scangle_it

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