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- PDB-4gre: DNA holliday junction stabilized by iodine halogen bond. I2J Cons... -

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Basic information

Entry
Database: PDB / ID: 4gre
TitleDNA holliday junction stabilized by iodine halogen bond. I2J Construct of 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*(IOU)P*CP*GP*G)-3')
KeywordsDNA / DNA Holliday junction / halogen bond
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Feb 28, 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

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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*(IOU)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
Water1,33374
1
A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(IOU)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*(IOU)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)12,4064
Polymers12,4064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area620 Å2
ΔGint-3 kcal/mol
Surface area4210 Å2
Unit cell
Length a, b, c (Å)64.956, 24.773, 37.616
Angle α, β, γ (deg.)90.00, 111.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

21B-114-

HOH

31B-132-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*GP*TP*AP*(IOU)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.: 74 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
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 298 K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→19.57 Å / Num. all: 6266 / Num. obs: 5772 / % possible obs: 91.4 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.9 Å2
Reflection shellResolution: 1.7→1.81 Å / % possible all: 78.2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.57 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 49861 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 619 10.7 %RANDOM
Rwork0.239 ---
all-6319 --
obs-5772 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.175 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 42.81 Å2 / Biso mean: 18.0466 Å2 / Biso min: 1.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å2-0.59 Å2
2--5.47 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 74 478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 98 11.9 %
Rwork0.266 724 -
all-822 -
obs--78.2 %
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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