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- PDB-1d56: ALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE ST... -

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Basic information

Entry
Database: PDB / ID: 1d56
TitleALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE STRUCTURE OF THE B-DNA DECAMER C-G-A-T-A-T-A-T-C-G
ComponentsDNA (5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsYuan, H. / Quintana, J. / Dickerson, R.E.
Citation
Journal: Biochemistry / Year: 1992
Title: Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G.
Authors: Yuan, H. / Quintana, J. / Dickerson, R.E.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: The Structure of B-Helical C-G-A-T-C-G-A-T-C-G and Comparison with C-C-A-A-C-G-T-T-G-G. The Effect of Base Pair Reversals
Authors: Grzeskowiak, K. / Yanagi, K. / Prive, G.G. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Analysis of Local Helix Geometry in Three B-DNA Decamers and Eight Dodecamers
Authors: Yanagi, K. / Prive, G.G. / Dickerson, R.E.
History
DepositionFeb 19, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 15, 1992Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1283
Polymers6,0882
Non-polymers401
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.760, 40.060, 33.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: pH 6.90, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CA ACETATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.33 mMDNA1drop
2140 mMcalcium acetate1drop
30.66 mMspermine-HCl1drop
410 %(v/v)MPD1drop
545 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→8 Å / Num. all: 6166 / Num. obs: 3683 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Observed criterion σ(F): 2
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 25 %

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.178 3683
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 8 87 499
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_planar_d
X-RAY DIFFRACTIONx_plane_restr0.0140.02
X-RAY DIFFRACTIONx_chiral_restr0.0730.1

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