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- PDB-2org: Directing Macromolecular Conformation Through Halogen Bonds -

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Basic information

Entry
Database: PDB / ID: 2org
TitleDirecting Macromolecular Conformation Through Halogen Bonds
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*TP*AP*(BRU)P*CP*GP*G)-3')
KeywordsDNA / DNA Holliday Junction / Halogen Bond
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVoth, A.R. / Hays, F.A. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Directing macromolecular conformation through halogen bonds.
Authors: Voth, A.R. / Hays, F.A. / Ho, P.S.
History
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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*(BRU)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)6,1562
Polymers6,1562
Non-polymers00
Water1,910106
1
A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(BRU)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')

A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(BRU)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)12,3124
Polymers12,3124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)65.779, 24.403, 37.316
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-52-

HOH

DetailsThe second half of the biological assembly (the Holliday junction) is generated by the two fold rotation: -x, y, -z+1

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Components

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


Mass: 3125.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetically prepared decanucleotide sequences.
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 43.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 mM sodium cacodylate, 20 mM calcium chloride, 1.2 mM spermine, and 0.35 mM of each DNA strand., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2calcium chloride11
3spermine11
4sodium cacodylate12
5calcium chloride12
6spermine12

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2004 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→18.2 Å / Num. all: 3852 / Num. obs: 3362 / % possible obs: 87.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.3 / Num. unique all: 382 / % possible all: 49.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P54

1p54


Resolution: 2→18.2 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 43547.84 / Data cutoff high rms absF: 43547.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 314 9.8 %RANDOM
Rwork0.218 ---
all0.247 3521 --
obs0.218 3200 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.7022 Å2 / ksol: 0.357361 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 106 510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
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→2.09 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 28 15.4 %
Rwork0.283 241 -
obs-196 49.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2ion.paramdna-rna.link
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.top

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