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- PDB-3fqb: Barium interactions with Z-DNA -

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Basic information

Entry
Database: PDB / ID: 3fqb
TitleBarium interactions with Z-DNA
Components
  • 5'-D(*CP*AP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*TP*G)-3'
KeywordsDNA / Z-DNA Double Helix
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMandal, P.K. / Venkadesh, S. / Vinayak, N. / Gautham, N.
CitationJournal: To be published
Title: Barium-DNA interactions
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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*AP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7573
Polymers3,6192
Non-polymers1371
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-13 kcal/mol
Surface area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.544, 30.512, 44.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*GP*TP*G)-3'


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.63 Å3/Da / Density % sol: 24.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: 50mM Sodium cacoldylate, 10mM Barium chloride, 0.5mM Spermine, 30% (v/v) Methyl pentane diol , pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacoldylate11
2Barium chloride11
3Spermine11
4MPD11
5Sodium cacoldylate12
6Barium chloride12
7MPD12

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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: Sep 17, 2008 / 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: 1.67→30 Å / Num. all: 3037 / Num. obs: 2791 / % possible obs: 91.9 % / Redundancy: 4.54 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.0882 / Rsym value: 0.0635 / Net I/σ(I): 6.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 4.37 % / Rmerge(I) obs: 0.2711 / Mean I/σ(I) obs: 1.7 / Num. unique all: 183 / Rsym value: 0.233 / % possible all: 89.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→13.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.983 / SU ML: 0.091 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22312 145 5.6 %RANDOM
Rwork0.21689 ---
obs0.2173 2427 86.05 %-
all-2427 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: LAST / Resolution: 1.67→13.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 249 2 39 290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021280
X-RAY DIFFRACTIONr_angle_refined_deg2.2473434
X-RAY DIFFRACTIONr_chiral_restr0.0940.249
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02125
X-RAY DIFFRACTIONr_nbd_refined0.2120.2112
X-RAY DIFFRACTIONr_nbtor_refined0.2740.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.218
X-RAY DIFFRACTIONr_metal_ion_refined0.40.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.23
X-RAY DIFFRACTIONr_scbond_it1.9253309
X-RAY DIFFRACTIONr_scangle_it2.5834.5431
LS refinement shellResolution: 1.673→1.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 12 -
Rwork0.32 183 -
obs-12 94.2 %

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