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- PDB-9dna: CRYSTAL STRUCTURE ANALYSIS OF AN A-DNA FRAGMENT AT 1.8 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 9dna
TitleCRYSTAL STRUCTURE ANALYSIS OF AN A-DNA FRAGMENT AT 1.8 ANGSTROMS RESOLUTION. D(GCCCGGGC)
ComponentsDNA (5'-D(*GP*CP*CP*CP*GP*GP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHeinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 1987
Title: Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).
Authors: Heinemann, U. / Lauble, H. / Frank, R. / Blocker, H.
History
DepositionJul 10, 1987Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water61334
1
A: DNA (5'-D(*GP*CP*CP*CP*GP*GP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)43.250, 43.250, 24.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: THE DEOXYRIBOSE PORTION OF RESIDUE C A 8 ADOPTS A SUGAR PUCKER IN THE C3(PRIME) -EXO DOMAIN. THIS IS UNUSUAL FOR THE A-DNA CONFORMATION.

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Components

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


Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DEOXYRIBOSE PORTION OF RESIDUE C A 8 ADOPTS A SUGAR PUCKER IN THE C3(PRIME) -EXO DOMAIN. THIS ...THE DEOXYRIBOSE PORTION OF RESIDUE C A 8 ADOPTS A SUGAR PUCKER IN THE C3(PRIME) -EXO DOMAIN. THIS IS UNUSUAL FOR THE A-DNA CONFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growMethod: microdialysis / Details: MICRODIALYSIS / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD OR ISOPROPANOL11
3BIS-TRIS-PROPANE_HCL11
4NA CACODYLATE11
5MGCL211
6WATER12
7MPD OR ISOPROPANOL12
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsChemical formulaSol-ID
110 mg/mlDNA1
210 mMTris-HCl1can be replaced with 20mM Na-cacodylate
310 mM1MgCl2
4MPD1can be replaced with isopropanol2
51
61
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: STOE / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. all: 2599 / Num. obs: 1553 / Observed criterion σ(I): 1
Reflection
*PLUS
Observed criterion σ(I): 1 / Rmerge(I) obs: 0.027 / Num. measured all: 2599

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.171 1359
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 34 195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.011
X-RAY DIFFRACTIONn_angle_d0.033
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 1359 / σ(F): 3 / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0110.025
X-RAY DIFFRACTIONn_angle_d0.0330.05
X-RAY DIFFRACTIONn_plane_restr0.0180.03
X-RAY DIFFRACTIONn_chiral_restr0.0440.1

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