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- PDB-1d61: THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINI... -

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Basic information

Entry
Database: PDB / ID: 1d61
TitleTHE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINIC FORM
ComponentsDNA (5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyCACODYLATE ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsLipanov, A. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Quintana, J. / 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. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Quintana, J. / Dickerson, R.E.
#1: Journal: Science / Year: 1992
Title: Helix Geometry, Hydration, and G.A Mismatch in a B-DNA Decamer
Authors: Prive, G.G. / Heinemann, U. / Chandrasegaran, S. / Kan, L.S. / Kopka, M.L. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallographic Study of One Turn of G/C-Rich B-DNA
Authors: Heinemann, U. / Alings, C.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of the B-DNA Decamer C-C-A-A-C-G-T-T-G-G and Comparison with 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.
History
DepositionFeb 26, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 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_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,2073
Polymers3,0301
Non-polymers1772
Water1,42379
1
A: DNA (5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,4146
Polymers6,0602
Non-polymers3544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)31.870, 25.690, 34.210
Angle α, β, γ (deg.)90.00, 114.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

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Components

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


Mass: 3029.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CA CACODYLATE11
4NA CACODYLATE11
5SPERMIDINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / 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
71

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Data collection

DiffractionMean temperature: 248 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→8 Å / Num. all: 5848 / Num. obs: 5026 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Num. measured all: 5848

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.3→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.152 5026
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL IONSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 4 79 284
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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