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- PDB-4e4o: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4e4o
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: 1.72 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 13, 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

Downloads & links

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


Theoretical massNumber of molelcules
Total (without water)7,3765
Polymers7,2394
Non-polymers1371
Water1,02757
1
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area2340 Å2
MethodPISA
2
C: DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-11 kcal/mol
Surface area2390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.055, 31.011, 31.368
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Mass: 1825.216 Da / Num. of mol.: 2 / 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.: 57 / 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: 1.5809 Å3/Da / Density % sol: 22.1971 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: drop: 1mM of duplex DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM barium dichloride dihydrate, 0.5mM spermine, reservoir: 30% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, ...Details: drop: 1mM of duplex DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM 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: Oct 6, 2010 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→25 Å / Num. all: 4897 / Num. obs: 4873 / % possible obs: 99.5 % / Redundancy: 4.71 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0384 / Rsym value: 0.0357 / Net I/σ(I): 9
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 4.68 % / Rmerge(I) obs: 0.2076 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.1908 / % possible all: 99.2

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Processing

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

Resolution: 1.72→23.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.645 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25709 228 4.7 %RANDOM
Rwork0.20126 ---
all0.23 4668 --
obs0.20373 4645 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.72→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 1 57 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3963868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2230.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.93560
X-RAY DIFFRACTIONr_scangle_it2.5324.5862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 21 -
Rwork0.256 317 -
obs--98.54 %

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