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- PDB-3hs1: Structure of Holliday junction formed by d(CCGGTACCGG); Crystal g... -

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Basic information

Entry
Database: PDB / ID: 3hs1
TitleStructure of Holliday junction formed by d(CCGGTACCGG); Crystal grown with CoCl2
Components5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
KeywordsDNA / Junction with B-DNA arms
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Crystal structure of Holliday junction
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water34219
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_556-x,y,-z+11
Buried area2720 Å2
ΔGint-7 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.002, 24.760, 37.369
Angle α, β, γ (deg.)90.00, 110.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-20-

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.: 19 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM Sodium Cacodylate buffer, 1mM CoCl2, 10mM spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2009 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→28.44 Å / Num. all: 1893 / Num. obs: 1864 / % possible obs: 92.9 % / Observed criterion σ(I): 1 / Redundancy: 2.84 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.075 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 1.4 / Num. unique all: 172 / Rsym value: 0.262 / % possible all: 90.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1JUC

1juc


Resolution: 2.51→28.44 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.977 / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.671 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25408 104 5.6 %RANDOM
Rwork0.23971 ---
all0.24057 1864 --
obs0.24057 1760 92.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.891 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20.01 Å2
2--1.65 Å20 Å2
3----0.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.472 Å
Refinement stepCycle: LAST / Resolution: 2.51→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 19 423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021452
X-RAY DIFFRACTIONr_angle_refined_deg2.8283694
X-RAY DIFFRACTIONr_chiral_restr0.1050.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02210
X-RAY DIFFRACTIONr_nbd_refined0.2680.2107
X-RAY DIFFRACTIONr_nbtor_refined0.3480.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.28
X-RAY DIFFRACTIONr_scbond_it2.4793666
X-RAY DIFFRACTIONr_scangle_it2.5274.5694
LS refinement shellResolution: 2.506→2.57 Å / Rfactor Rfree error: 0.327 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.803 5 -
Rwork0.46 110 -
obs-110 88.46 %

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