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- PDB-4e2r: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4e2r
TitleInteractions of Ba2+ with a non-self-complementary Z-type DNA duplex
Components
  • DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
KeywordsDNA / Z-type DNA double helices / Barium ions
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: To be Published
Title: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,7573
Polymers3,6192
Non-polymers1371
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 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 DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')


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


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized short NA strand
#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.: 44 / 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: 1.6346 Å3/Da / Density % sol: 24.7532 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: drop: 50mM sodium cacodylate trihydrate buffer (pH 7.0), 10mM barium dichloride dihydrate, 0.5mM spermine, reservoir: 30% 2-methyl-2,4-pentanediol (MPD), 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 11, 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: 1.67→30 Å / Num. all: 3022 / Num. obs: 2778 / % possible obs: 92 % / Redundancy: 4.54 % / Biso Wilson estimate: 26.1 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: 258 / Rsym value: 0.233 / % possible all: 89.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fiber model of Z-type DNA built using the program InsightII

Resolution: 1.67→25.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.807 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22691 119 4.6 %RANDOM
Rwork0.18691 ---
obs0.18898 2453 85.48 %-
all-2869 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.67→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 1 44 285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021276
X-RAY DIFFRACTIONr_angle_refined_deg1.9193426
X-RAY DIFFRACTIONr_chiral_restr0.0750.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02126
X-RAY DIFFRACTIONr_scbond_it1.7983276
X-RAY DIFFRACTIONr_scangle_it2.4754.5424
LS refinement shellResolution: 1.673→1.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.126 5 -
Rwork0.246 189 -
obs--88.99 %

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