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- PDB-256d: ALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE... -

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Basic information

Entry
Database: PDB / ID: 256d
TitleALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE AS CANONICAL A-DNA
ComponentsDNA (5'-D(*GP*(5CM)P*GP*CP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMooers, B.H. / Schroth, G.P. / Baxter, W.W. / Ho, P.S.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA.
Authors: Mooers, B.H. / Schroth, G.P. / Baxter, W.W. / Ho, P.S.
History
DepositionMar 31, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 15, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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(*GP*(5CM)P*GP*CP*GP*C)-3')
B: DNA (5'-D(*GP*(5CM)P*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,6482
Polymers3,6482
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.440, 45.840, 39.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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


Mass: 1824.232 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE11
5MGCL211
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMDNA1drop
215 mMsodium cacodylate1drop
30.5-5. mMspermine1drop
41-20 mM1dropMgCl2
55 %(v/v)MPD1drop
635 %MPD1reservoir
71

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Data collection

Diffraction sourceSource: SEALED TUBE
DetectorType: SIEMENS P4 / Detector: DIFFRACTOMETER / Date: Feb 21, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 2102 / Num. obs: 1713 / % possible obs: 75 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % possible obs: 75 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORrefinement
XSCANSdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.148 --
all0.165 --
obs0.148 1273 64.1 %
Displacement parametersBiso mean: 11.1 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 2 35 277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg4.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d35
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg35
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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