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- PDB-400d: THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE ... -

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Basic information

Entry
Database: PDB / ID: 400d
TitleTHE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA
ComponentsDNA (5'-D(*(5CM)P*GP*GP*CP*(5CM)P*G)-3')
KeywordsDNA / Z-DNA DOUBLE HELIX
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsEichman, B.F. / Basham, B. / Schroth, G.P. / Ho, P.S.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA.
Authors: Eichman, B.F. / Schroth, G.P. / Basham, B.E. / Ho, P.S.
History
DepositionMay 28, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 9, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 3, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Feb 28, 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(*(5CM)P*GP*GP*CP*(5CM)P*G)-3')
B: DNA (5'-D(*(5CM)P*GP*GP*CP*(5CM)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
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)17.790, 30.900, 44.360
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(*(5CM)P*GP*GP*CP*(5CM)P*G)-3')


Mass: 1838.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.66 Å3/Da / Density % sol: 25.82 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.3 mMDNA1dropsingle stranded
212 mMsodium cacodylate1drop
325 mM1dropMgCl2
41 mMspermine tetrachloride1drop
55 %(v/v)MPD1drop
630 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: SIEMENS / Detector: DIFFRACTOMETER / Date: Jun 1, 1992
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 3197 / Observed criterion σ(I): 3 / Redundancy: 10 % / Rmerge(I) obs: 0.03
Reflection
*PLUS
Highest resolution: 1.65 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XSCANSdata reduction
XSCANSdata scaling
RefinementResolution: 1.65→8 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.248 -10 %
Rwork0.196 --
obs0.196 1875 -
Refine Biso Class: 1
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 4 35 279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 1.93→2.07 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.326 -9 %
Rwork0.23 187 -
obs--53.1 %
Xplor fileSerial no: 1 / Param file: DNA-RNA.PARAM / Topol file: DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.3263 / % reflection Rfree: 9 % / Rfactor Rwork: 0.2298

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