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- PDB-1juc: Crystal Structure Analysis of a Holliday Junction Formed by CCGGTACCGG -

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Basic information

Entry
Database: PDB / ID: 1juc
TitleCrystal Structure Analysis of a Holliday Junction Formed by CCGGTACCGG
Components5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
KeywordsDNA / HOLLIDAY JUNCTION
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsThorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Cardin, C.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?
Authors: Thorpe, J.H. / Teixeira, S.C. / Gale, B.C. / Cardin, C.J.
History
DepositionAug 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water77543
1
A: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'

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


Theoretical massNumber of molelcules
Total (without water)12,1844
Polymers12,1844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)64.871, 25.364, 37.373
Angle α, β, γ (deg.)90.00, 110.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-140-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.24 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40 mM sodium cacodylate (pH 7.0), 12 mM spermine, 80 mM KCl, 10% (v/v) MPD equilibrated against 35% MPD with oligo concentration of 1 mM, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2spermine11
4KCl11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 290 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mM1droppH7.0
212 mM1drop
480 mM1dropKCl
510 %(v/v)1drop
61 mMd(CCGGTACCGG)21drop
735 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.073 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 4339 / Num. obs: 2387 / % possible obs: 96.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.267 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 2390 / % possible obs: 96.41 % / Num. measured all: 4466 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.37

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Processing

Software
NameVersionClassification
XFITdata reduction
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.35→34.92 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.952 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26779 104 4.4 %RANDOM
Rwork0.22639 ---
obs0.22841 2286 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.349 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å2-0.01 Å2
2--3.32 Å20 Å2
3----0.41 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 426
Refinement stepCycle: LAST / Resolution: 2.35→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 43 447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0670.021452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02181
X-RAY DIFFRACTIONr_angle_refined_deg2.1953694
X-RAY DIFFRACTIONr_angle_other_deg1.4633459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.5180.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0330.02208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.3131
X-RAY DIFFRACTIONr_nbd_other0.3290.3226
X-RAY DIFFRACTIONr_nbtor_other0.1570.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.5230.531
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 7
Rwork0.297 157
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.067
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.195
LS refinement shell
*PLUS
Rfactor Rfree: 0.44 / Total num. of bins used: 20 / Rfactor obs: 0.31

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