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- PDB-1dn8: STRUCTURE OF A Z-DNA WITH TWO DIFFERENT BACKBONE CHAIN CONFORMATI... -

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Basic information

Entry
Database: PDB / ID: 1dn8
TitleSTRUCTURE OF A Z-DNA WITH TWO DIFFERENT BACKBONE CHAIN CONFORMATIONS. STABILIZATION OF THE DECADEOXYOLIGONUCLEOTIDE D(CGTACGTACG) BY (CO(NH3)6)3+ BINDING TO THE GUANINE
ComponentsDNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsBrennan, R.G. / Westhof, E. / Sundaralingam, M.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 1986
Title: Structure of a Z-DNA with two different backbone chain conformations. Stabilization of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine.
Authors: Brennan, R.G. / Westhof, E. / Sundaralingam, M.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization and Preliminary Crystallographic Studies of the Decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG)
Authors: Brennan, R.G. / Sundaralingam, M.
History
DepositionMay 12, 1987Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*TP*AP*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3383
Polymers1,1772
Non-polymers1611
Water00
1
A: DNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3')
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)8,02818
Polymers7,06112
Non-polymers9676
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+5/61
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation5_555y,-x+y,z+1/61
Unit cell
Length a, b, c (Å)17.930, 17.930, 43.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 588.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28.14 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 279.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PROPANOL11
3SPERMINE11
4[CO(NH3)6]CL311
5WATER12
6PROPANOL12
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
11.5 mMdeoxydecamer1
20.625 mMspermine1
31.67 mM1Co(NH3)6Cl3
430 %(v/v)n-propanol1reservoir
51
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. all: 1250 / Num. obs: 506 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.5 Å / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å / Occupancy max: 1 / Occupancy min: 0.01 / σ(F): 2 /
RfactorNum. reflection
obs0.25 506
Refine Biso
ClassRefine-IDDetailsTreatment
1X-RAY DIFFRACTION
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
(CH3) ON THYMINEX-RAY DIFFRACTIONTRisotropic
(NH2) ON ADENINEX-RAY DIFFRACTIONTRisotropic
PO4 5PRIME TO PYX-RAY DIFFRACTIONTRisotropic
[CO(NH3)6]3+X-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.5→10 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 84 7 0 91
Refinement
*PLUS
Highest resolution: 1.5 Å / Num. reflection obs: 506 / σ(F): 2 / Rfactor obs: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS

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