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- PDB-1s1l: Influence of Groove Interactions on the Formation of DNA Holliday... -

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Basic information

Entry
Database: PDB / ID: 1s1l
TitleInfluence of Groove Interactions on the Formation of DNA Holliday Junctions
Components5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
KeywordsDNA / Holliday Junction / DNA Four-Way Junction / major groove / Inosine / minor groove
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHays, F.A. / Jones, Z.J. / Ho, P.S.
CitationJournal: Biochemistry / Year: 2004
Title: Influence of minor groove substituents on the structure of DNA holliday junctions.
Authors: Hays, F.A. / Jones, Z.J. / Ho, P.S.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE FULL BIOLOGICAL UNIT CONSISTS OF A FOUR STRANDED DNA HOLLIDAY JUNCTION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water1,11762
1
A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'

A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)12,1804
Polymers12,1804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)64.923, 24.869, 37.095
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-49-

HOH

DetailsFull four stranded Holliday junction structure is generated by a 2-fold symmetry axis.

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Components

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


Mass: 3045.006 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 25mM Na Cacodylate, .5mM DNA, 180mM CaCl2, 2.4mM spermine against 20% resevoir MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2.5mM DNA11
3CaCl211
4spermine11
5MPD12
6Na Cacodylate12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2003 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→18.2 Å / Num. all: 3492 / Num. obs: 3492 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.4 / % possible all: 61.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ndb id UD0019

Resolution: 2.2→18.2 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 44978.75 / Data cutoff high rms absF: 44978.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 286 10 %RANDOM
Rwork0.236 ---
all0.266 3492 --
obs0.236 2852 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3728 Å2 / ksol: 0.360393 e/Å3
Displacement parametersBiso mean: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å2-1.93 Å2
2--2.33 Å20 Å2
3----4.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 62 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 40 9.3 %
Rwork0.267 391 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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