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- PDB-390d: STRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-D... -

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Basic information

Entry
Database: PDB / ID: 390d
TitleSTRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-DNA IN CRYSTALS OF D(PCPGPCPGPCPG)
ComponentsDNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMalinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y.
CitationJournal: Biophys.J. / Year: 1998
Title: Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).
Authors: Malinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y.
History
DepositionApr 20, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0May 5, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,4313
Polymers5,4313
Non-polymers00
Water75742
1
A: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')

C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)69.730, 52.630, 26.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

21C-301-

HOH

31C-326-

HOH

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Components

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


Mass: 1810.205 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE TETRACLORIDE11
3NA CACODYLATE11
42-METHYL-2,4-PENTANEDIOL11
5WATER12
62-METHYL-2,4-PENTANEDIOL12
Crystal grow
*PLUS
Method: other / Details: Malinina, L., (1991) J. Crystal Growth, 110, 252.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER / Date: Jan 1, 1988
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34.9 Å / Num. obs: 3248 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 34.9 Å / % possible obs: 93 % / Rmerge(I) obs: 0.026

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SYNTEXP21data reduction
SYNTEXP21data scaling
RefinementResolution: 2→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -10 %RANDOM
Rwork0.188 ---
all0.192 3172 --
obs0.188 3171 93 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 372 0 42 414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.44
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 309 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61

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