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- PDB-1ofx: CRYSTAL STRUCTURE OF AN OKAZAKI FRAGMENT AT 2 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ofx
TitleCRYSTAL STRUCTURE OF AN OKAZAKI FRAGMENT AT 2 ANGSTROMS RESOLUTION
Components
  • DNA (5'-D(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3')
  • DNA/RNA (5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*CP*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologySPERMINE / DNA / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEgli, M. / Usman, N. / Zhang, S. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal structure of an Okazaki fragment at 2-A resolution.
Authors: Egli, M. / Usman, N. / Zhang, S.G. / Rich, A.
History
DepositionOct 17, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1993Provider: 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 / 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(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3403
Polymers6,1382
Non-polymers2021
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.030, 43.670, 48.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*CP*C)-3')


Mass: 3052.981 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mMOkazaki fragment1drop
230 mMsodium cacodylate1drop
37.8 mMmagnesium chloride1drop
475 mMspermine tetrachloride1drop
540 %(v/v)MPD1reservoir
61

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Data collection

DiffractionMean temperature: 163 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 3858 / Num. obs: 1860 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.156 1826
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTFisotropic
ALL WATERSX-RAY DIFFRACTIONTFisotropic
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 407 14 93 514
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg1

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