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- PDB-3ana: THREE-DIMENSIONAL STRUCTURE OF D(GGGATCCC) IN THE CRYSTALLINE STATE -

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Basic information

Entry
Database: PDB / ID: 3ana
TitleTHREE-DIMENSIONAL STRUCTURE OF D(GGGATCCC) IN THE CRYSTALLINE STATE
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHeinemann, U. / Lauble, H.
CitationJournal: Nucleic Acids Res. / Year: 1988
Title: Three-dimensional structure of d(GGGATCCC) in the crystalline state.
Authors: Lauble, H. / Frank, R. / Blocker, H. / Heinemann, U.
History
DepositionJul 6, 1988Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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(*GP*GP*GP*AP*TP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.830, 46.830, 44.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growMethod: microdialysis / Details: MICRODIALYSIS / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mMDNA1
224 %(v/v)12
320 mMsodium cacodylate1
45 mMmagnesium chloride1
51
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: STOE / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 4130 / Num. obs: 1594 / Observed criterion σ(I): 1
Reflection
*PLUS
Num. obs: 1300 / % possible obs: 78 % / Rmerge(I) obs: 0.029 / Num. measured all: 1594

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.166 1428
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 9 331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d0.034
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_d0.011
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.04
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
σ(F): 3 / Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 1428 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONn_bond_d0.05
X-RAY DIFFRACTIONn_angle_d0.050.034
X-RAY DIFFRACTIONn_plane_restr0.030.013
X-RAY DIFFRACTIONn_chiral_restr0.10.055

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