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- PDB-3gom: Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4 -

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Basic information

Entry
Database: PDB / ID: 3gom
TitleBarium bound to the Holliday junction sequence d(TCGGCGCCGA)4
Components5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
KeywordsDNA / Holliday junction structure
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNaseer, A. / Cardin, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
Authors: Hall, J.P. / O'Sullivan, K. / Naseer, A. / Smith, J.A. / Kelly, J.M. / 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 2, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,7797
Polymers6,0922
Non-polymers6875
Water64936
1
A: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
B: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)13,55714
Polymers12,1844
Non-polymers1,37310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5740 Å2
ΔGint-98 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.2000, 23.8000, 37.4100
Angle α, β, γ (deg.)90.0000, 110.0100, 90.0000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3045.992 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.: 5 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
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: multigraded optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→19.956 Å / Num. all: 2518 / Num. obs: 2351 / % possible obs: 93.22 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 31.247 Å2 / Limit h max: 26 / Limit h min: -28 / Limit k max: 10 / Limit k min: 0 / Limit l max: 16 / Limit l min: 0 / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.21 / Num. unique all: 461 / % possible all: 93.22

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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 1NVY

1nvy


Resolution: 2.3→19.956 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 13.5 / SU ML: 0.291 / SU R Cruickshank DPI: 0.604 / Cross valid method: THROUGHOUT / ESU R Free: 0.371
RfactorNum. reflection% reflectionSelection details
Rfree0.349 101 4.3 %RANDOM
Rwork0.26 ---
all0.264 2351 --
obs0.264 2351 93.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.247 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å2-0.97 Å2
2--3.16 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 5 36 445
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0084520.021
X-RAY DIFFRACTIONr_angle_refined_deg1.8226943
X-RAY DIFFRACTIONr_chiral_restr0.066780.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0062080.02
X-RAY DIFFRACTIONr_nbd_refined0.1931210.2
X-RAY DIFFRACTIONr_nbtor_refined0.3162590.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.325280.2

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