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- PDB-6a1o: Crystal structures of disordered Z-type helices -

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Basic information

Entry
Database: PDB / ID: 6a1o
TitleCrystal structures of disordered Z-type helices
Components
  • DNA (5'-D(P*CP*A)-3')
  • DNA (5'-D(P*CP*AP*CP*A)-3')
  • DNA (5'-D(P*TP*G)-3')
  • DNA (5'-D(P*TP*GP*TP*G)-3')
KeywordsDNA / Decameric sequence / left handed Z-DNA duplex / discontinuous helices / hexagonal space group
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsKarthik, S. / Mandal, P.K. / Thirugnanasambandam, A. / Gautham, N.
CitationJournal: Nucleosides Nucleotides Nucleic Acids / Year: 2019
Title: Crystal structures of disordered Z-type helices.
Authors: Karthik, S. / Mandal, P.K. / Thirugnanasambandam, A. / Gautham, N.
History
DepositionJun 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / pdbx_related_exp_data_set / Item: _citation.title
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,5284
Polymers3,5284
Non-polymers00
Water543
1
A: DNA (5'-D(P*TP*G)-3')
B: DNA (5'-D(P*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)1,1462
Polymers1,1462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-2 kcal/mol
Surface area1120 Å2
MethodPISA
2
C: DNA (5'-D(P*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)2,3822
Polymers2,3822
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-5 kcal/mol
Surface area1760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.112, 31.112, 43.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 588.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*A)-3')


Mass: 557.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*TP*G)-3')


Mass: 1221.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*AP*CP*A)-3')


Mass: 1159.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.7 Å3/Da / Density % sol: 27.85 %
Description: Authors state that the packing requirement imposes statistical disorder in the molecule leading to only a portion of the molecule to be present in asymmetric unit (One tetramer and a ...Description: Authors state that the packing requirement imposes statistical disorder in the molecule leading to only a portion of the molecule to be present in asymmetric unit (One tetramer and a dinucleotide step). Hence the terminal phosphate atoms appears to be in close contact with the symmetry related terminal oxygens.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM sodium cacodylate trihydrate buffer, 50mM CaCl2, 50% MPD.

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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 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.51
ReflectionResolution: 2.49→16.816 Å / Num. obs: 1584 / % possible obs: 97.1 % / Redundancy: 4.384 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Χ2: 0.954 / Net I/σ(I): 9.95 / Num. measured all: 6944
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.644.3970.1716.242570.9890.19497
2.64-2.814.3970.1995.722320.9810.22695.5
2.81-3.034.3860.1237.652150.9950.1496.4
3.03-3.314.3960.1038.812070.9950.11897.2
3.31-3.684.4240.08112.261720.9960.09397.2
3.68-4.224.3410.0713.571700.9980.0898.8
4.22-5.094.3490.06615.231490.9960.07598.7
5.09-6.894.3580.07315.811090.9920.083100
6.89-16.8164.370.05613.12730.9990.06592.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å14.63 Å
Translation3 Å14.63 Å

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Processing

Software
NameVersionClassification
XDSGPLv2data reduction
XDSGPLv2data scaling
PHASER2.6.0phasing
PHENIX1.10.1-2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D53

1d53


Resolution: 2.49→16.816 Å / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 35.61
RfactorNum. reflection% reflection
Rfree0.2994 161 10.16 %
Rwork0.2799 --
obs0.2745 1584 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.02 Å2 / Biso mean: 21.6559 Å2 / Biso min: 5.61 Å2
Refinement stepCycle: final / Resolution: 2.49→16.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 246 0 3 249
Biso mean---55.06 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009272
X-RAY DIFFRACTIONf_angle_d1.236410
X-RAY DIFFRACTIONf_chiral_restr0.08948
X-RAY DIFFRACTIONf_plane_restr0.00512
X-RAY DIFFRACTIONf_dihedral_angle_d33.515108
LS refinement shellResolution: 2.5068→14.6302 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2882 160 -
Rwork0.2722 1394 -
all-1554 -
obs--87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.047-0.00970.01940.0014-0.00460.0105-0.0112-0.00160.02050.0096-0.02640.0305-0.035-0.0253-0.02260.27040.1189-0.08070.336-0.2087-0.085712.498930.7529-21.6086
20.05880.01440.06690.08780.02640.0766-0.0149-0.0020.0026-0.009-0.0113-0.0146-0.00160.0422-0.01840.07140.03540.16870.2822-0.13210.298720.617526.0683-22.8904
30.00440.00510.01390.0090.02440.0603-0.0115-0.02110.00290.007-0.03570.0036-0.03350.0114-0.02810.06540.0214-0.0940.0843-0.0571-0.022330.936340.2699-18.6792
40.00920.00330.00860.03720.00490.0068-0.00390.0239-0.0071-0.0018-0.024-0.0170.02040.035-0.02310.07580.00330.15590.1437-0.0454-0.256434.064932.8064-20.041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 2 )A1 - 2
2X-RAY DIFFRACTION2chain 'B' and (resid 3 through 4 )B3 - 4
3X-RAY DIFFRACTION3chain 'C' and (resid 5 through 8 )C5 - 8
4X-RAY DIFFRACTION4chain 'D' and (resid 9 through 12 )D9 - 12

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