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- PDB-145d: Structure and thermodynamics of nonalternating C/G base pairs in ... -

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Entry
Database: PDB / ID: 145d
TitleStructure and thermodynamics of nonalternating C/G base pairs in Z-DNA: the 1.3 angstroms crystal structure of the asymmetric hexanucleotide D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG)
Components
  • DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3')
  • DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3')
  • DNA (5'-D(*(MCY)P*GP*GP*GP*(5CM)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.25 Å
AuthorsSchroth, G.P. / Kagawa, T.F. / Shing Ho, P.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG).
Authors: Schroth, G.P. / Kagawa, T.F. / Ho, P.S.
#1: Journal: Nucleic Acids Res. / Year: 1982
Title: Molecular Structure of (m5dC-dG)3: The Role of the Methyl Group on 5-Methyl Cytosine in Stabilizing Z-DNA
Authors: Fujii, S. / Wang, A.H.-J. / Van Der Marel, G. / Van Boom, J.H. / Rich, A.
History
DepositionNov 11, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1134
Polymers7,1134
Non-polymers00
Water86548
1
A: DNA (5'-D(*(MCY)P*GP*GP*GP*(5CM)P*G)-3')
B: DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,5172
Polymers3,5172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3')
D: DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3')


Theoretical massNumber of molelcules
Total (without water)3,5972
Polymers3,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.865, 30.822, 44.797
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(*(MCY)P*GP*GP*GP*(5CM)P*G)-3')


Mass: 1798.303 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3')


Mass: 1718.255 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3')


Mass: 1878.283 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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

Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMIDINE11
5WATER12
6MPD12

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: SIEMENS / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.25→8 Å / σ(F): 1.5 /
RfactorNum. reflection
obs0.193 5029
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 776 0 144 920
Refinement
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 8 Å / Num. reflection obs: 5029 / σ(F): 1.5 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.36 Å / Total num. of bins used: 8 / Num. reflection obs: 420 / Rfactor all: 0.1931

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