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- PDB-392d: STRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-D... -

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Basic information

Entry
Database: PDB / ID: 392d
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: 3 Å
AuthorsMalinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y.
Citation
Journal: 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.
#1: Journal: J.Biomol.Struct.Dyn. / Year: 1994
Title: A Simplified Multidimensional Search Used for Crystal Structure Sloution of pCpGpCpGpCpG with Two Duplexes per Asymmetric Unit
Authors: Strocopytov, B.V. / Malinina, L.V.
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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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


Theoretical massNumber of molelcules
Total (without water)7,2655
Polymers7,2414
Non-polymers241
Water00
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6453
Polymers3,6202
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.800, 37.300, 70.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL211
3SPERMINE TETRACLORIDE11
4NA CACODYLATE11
52-METHYL-2,4-PENTANEDIOL11
6WATER12
72-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
71

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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: 3→35.2 Å / Num. obs: 1276 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SYNTEXP21data reduction
SYNTEXP21data scaling
RefinementResolution: 3→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.182 ---
all0.188 1189 --
obs0.182 1144 92.1 %-
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 496 1 0 497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.57
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

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