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- PDB-3t8p: Crystal structure of d(CGGGTACCCG)4 as a four-way Holliday junction -

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Basic information

Entry
Database: PDB / ID: 3t8p
TitleCrystal structure of d(CGGGTACCCG)4 as a four-way Holliday junction
ComponentsDNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*CP*CP*G)-3')
KeywordsDNA / DNA four-way Holliday Junction / Recombination
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of d(CGGGTACCCG)(4) as a four-way Holliday junction
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1323
Polymers6,0922
Non-polymers401
Water32418
1
A: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*CP*CP*G)-3')
B: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*CP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,2646
Polymers12,1844
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.289, 23.597, 37.124
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 40mM sodium cacodylate, 85mM Calcium chloride, equilibrated against 30% methyl pentane diol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→34.59 Å / Num. obs: 2236 / % possible obs: 96.53 % / Redundancy: 2.83 % / Biso Wilson estimate: 53.13 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.0885 / Net I/σ(I): 3.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2236 / Rsym value: 0.249 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NT8

1nt8


Resolution: 2.35→34.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU ML: 0.169 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.57 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27839 112 5 %RANDOM
Rwork0.23546 ---
obs0.23759 2115 96.53 %-
all-2263 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.04 Å2
2--0.21 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 18 423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.983694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02210
X-RAY DIFFRACTIONr_nbd_refined0.2550.2106
X-RAY DIFFRACTIONr_nbtor_refined0.330.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.26
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 7 -
Rwork0.38 160 -
obs-160 97.66 %

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