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- PDB-3goj: Barium bound to the Holliday sequence d(CCGGCGCCGG)4 -

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Basic information

Entry
Database: PDB / ID: 3goj
TitleBarium bound to the Holliday sequence d(CCGGCGCCGG)4
Components5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
KeywordsDNA / Holliday junction structure
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNaseer, A. / Cardin, C.J.
CitationJournal: To be Published
Title: Barium bound to the Holliday junction structure
Authors: Naseer, A. / Cardin, C.J.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 6, 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: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6436
Polymers6,0942
Non-polymers5494
Water41423
1
A: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)13,28712
Polymers12,1884
Non-polymers1,0998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5020 Å2
ΔGint-72 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.2430, 24.2410, 37.2810
Angle α, β, γ (deg.)90.00, 110.1700, 90.0000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Holliday junction structure
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1BaCl211
2MPD11
3Na Cacodylate11
4BaCl212
5MPD12
6Na Cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Details: multilayer optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.601→15.615 Å / Num. all: 1772 / Num. obs: 1757 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 21.448 Å2 / Limit h max: 23 / Limit h min: -24 / Limit k max: 9 / Limit k min: 0 / Limit l max: 14 / Limit l min: 0 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.601→2.668 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.18 / Num. unique all: 6667 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.401data extraction
CrysalisProReddata collection
CrysalisProReddata reduction
CrysalisProReddata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P4Y

1p4y


Resolution: 2.6→15.615 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.111 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.466
RfactorNum. reflection% reflectionSelection details
Rfree0.347 74 4.2 %RANDOM
Rwork0.236 ---
all0.241 1757 --
obs0.241 1757 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.444 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20.45 Å2
2--3.29 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 4 23 431
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0094520.021
X-RAY DIFFRACTIONr_angle_refined_deg1.9036943
X-RAY DIFFRACTIONr_chiral_restr0.068780.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0072100.02
X-RAY DIFFRACTIONr_nbd_refined0.2181090.2
X-RAY DIFFRACTIONr_nbtor_refined0.3332520.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.272240.2
X-RAY DIFFRACTIONr_metal_ion_refined0.35130.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.168300.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.24190.2
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.32120.2
X-RAY DIFFRACTIONr_scbond_it1.5335103
X-RAY DIFFRACTIONr_scangle_it2.3246944.5
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 7 -
Rwork0.44 123 -
obs--99.24 %

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