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- PDB-4e60: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4.0E+60
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')
  • DNA (5'-D(P*TP*G)-3')
KeywordsDNA / Z-type DNA double helices / Barium ions
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _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')
C: DNA (5'-D(P*TP*G)-3')
D: DNA (5'-D(P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9345
Polymers4,7964
Non-polymers1371
Water27015
1
A: DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
B: 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 area860 Å2
ΔGint-13 kcal/mol
Surface area2320 Å2
MethodPISA
2
C: DNA (5'-D(P*TP*G)-3')
D: DNA (5'-D(P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3143
Polymers1,1772
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-5 kcal/mol
Surface area1070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.177, 35.177, 44.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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
#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
#3: DNA chain DNA (5'-D(P*TP*G)-3')


Mass: 588.441 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-BA / BARIUM ION


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.6512 Å3/Da / Density % sol: 25.5074 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: drop: 1mM DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 1mM 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 8, 2008 / 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: 1.86→30 Å / Num. all: 2655 / Num. obs: 2650 / % possible obs: 99.8 % / Redundancy: 6.49 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.094 / Net I/σ(I): 4.6
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.67 % / Rmerge(I) obs: 0.1724 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.1698 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
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: 1.86→25.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.275 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23147 119 4.5 %RANDOM
Rwork0.21524 ---
obs0.21601 2529 99.66 %-
all-2537 --
Displacement parametersBiso mean: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 321 1 15 337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.021357
X-RAY DIFFRACTIONr_angle_refined_deg3.493544
X-RAY DIFFRACTIONr_chiral_restr0.2130.261
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02170
X-RAY DIFFRACTIONr_scbond_it3.5733357
X-RAY DIFFRACTIONr_scangle_it4.3154.5544
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 8 -
Rwork0.307 179 -
obs--98.94 %

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