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- PDB-4gs2: DNA Holliday junction stabilized by iodine halogen bond. I1J cons... -

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Basic information

Entry
Database: PDB / ID: 4gs2
TitleDNA Holliday junction stabilized by iodine halogen bond. I1J construct in related reference.
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*TP*AP*(5IU)P*CP*GP*G)-3')
KeywordsDNA / DNA Holliday junction / halogen bond
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHo, P.S. / Carter, M.
CitationJournal: Biochemistry / Year: 2013
Title: Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.
Authors: Carter, M. / Voth, A.R. / Scholfield, M.R. / Rummel, B. / Sowers, L.C. / Ho, P.S.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,2032
Polymers6,2032
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.739, 25.187, 37.171
Angle α, β, γ (deg.)90.000, 110.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-112-

HOH

21A-125-

HOH

Details-x,y,-z

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Components

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


Mass: 3172.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetically engineered DNA sequence
#2: DNA chain DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')


Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 4645 / Num. obs: 3432 / % possible obs: 73.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.4 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ORG

2org


Resolution: 1.9→23.3 Å / Rfactor Rfree error: 0.014 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 378015 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.4 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 345 10.1 %RANDOM
Rwork0.235 ---
all-4645 --
obs-3423 73.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9687 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 51.95 Å2 / Biso mean: 31.4219 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--6.64 Å20 Å2-0.06 Å2
2--7.2 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 73 477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 49 10.1 %
Rwork0.353 436 -
all-485 -
obs--63.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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