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- PDB-6a1q: Crystal structures of disordered Z-type helices -

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Basic information

Entry
Database: PDB / ID: 6a1q
TitleCrystal structures of disordered Z-type helices
Components
  • DNA (5'-D(P*CP*AP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*TP*G)-3')
KeywordsDNA / Tetradecamer sequence / alternate pyr-pur repeat / left handed Z-DNA duplex / discontinuous helices / P3(2)
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 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: pdbx_related_exp_data_set
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*GP*TP*G)-3')
B: DNA (5'-D(P*CP*AP*CP*A)-3')
C: DNA (5'-D(P*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*A)-3')
E: DNA (5'-D(P*TP*GP*TP*G)-3')
F: DNA (5'-D(P*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,1456
Polymers7,1456
Non-polymers00
Water181
1
A: DNA (5'-D(P*TP*GP*TP*G)-3')
B: DNA (5'-D(P*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)2,3822
Polymers2,3822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-5 kcal/mol
Surface area1740 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 area450 Å2
ΔGint-4 kcal/mol
Surface area1760 Å2
MethodPISA
3
E: DNA (5'-D(P*TP*GP*TP*G)-3')
F: DNA (5'-D(P*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)2,3822
Polymers2,3822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-5 kcal/mol
Surface area1740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.675, 30.675, 42.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


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


Mass: 1159.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.61 Å3/Da / Density % sol: 23.61 %
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. Hence the terminal ...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. 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, 200mM MgSO4, 50% MPD.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.5→16.56 Å / Num. obs: 2962 / % possible obs: 95.9 % / Redundancy: 2.602 % / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.076 / Χ2: 1.02 / Net I/σ(I): 9.13 / Num. measured all: 7706
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.652.6190.1444.374620.9870.18195.1
2.65-2.832.6180.1265.764400.9840.15794.8
2.83-3.052.5890.0857.684310.9940.10596.6
3.05-3.322.6380.0637.923560.9960.07995.7
3.32-3.72.5870.06311.593580.9990.07696.8
3.7-4.242.60.05113.163050.9940.06496.5
4.24-5.12.5740.05213.582770.9940.06597.5
5.1-6.92.5660.05213.811960.9910.06697
6.9-16.562.5840.05712.681370.9970.07191.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å14.42 Å
Translation3 Å14.42 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSGPLv2data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
XDSGPLv2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P4J
Resolution: 2.501→16.56 Å / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 35.4
Details: It has to be noted that limited resolution data was available to refine the highly disordered molecules. The atomic coordinates are best interpreted for the data to a resolution of 2.5 A and ...Details: It has to be noted that limited resolution data was available to refine the highly disordered molecules. The atomic coordinates are best interpreted for the data to a resolution of 2.5 A and the electron density map is justified for this highly disordered in packing Z-type helices in which exocyclic atoms of the pyrimidine bases and backbone phosphate groups are refined with partial occupancies.
RfactorNum. reflection% reflection
Rfree0.2761 304 10.27 %
Rwork0.2741 --
obs0.2714 2961 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→16.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 1 493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014546
X-RAY DIFFRACTIONf_angle_d1.646828
X-RAY DIFFRACTIONf_dihedral_angle_d32.466222
X-RAY DIFFRACTIONf_chiral_restr0.11696
X-RAY DIFFRACTIONf_plane_restr0.00924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5147-3.16010.34161370.35191292X-RAY DIFFRACTION86
3.1601-12.67420.26151640.23531299X-RAY DIFFRACTION86
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.00950.00090.0101-0.0010.00180.016-0.11120.0369-0.0371-0.084-0.0314-0.0525-0.05920.1251-0.08070.0869-0.1360.00870.20580.13540.163650.005-7.0069-5.3086
20.0018-0.00080.001-0.0003-0.00260.0042-0.04820.00170.0169-0.0052-0.0112-0.0187-0.0624-0.1196-0.0110.18130.05530.04750.3171-0.08580.177742.005-7.9407-3.9062
30.0077-0.0062-0.00630.00460.00730.0112-0.03790.05560.0274-0.0077-0.0813-0.00990.02060.0886-0.07180.37230.09880.12120.36080.08490.0633.8163-20.44240.9343
40.02930.0006-0.00030.0696-0.07090.07370.0165-0.0023-0.00460.0402-0.05010.0324-0.06870.0217-0.05070.02080.04260.02590.0975-0.06450.083330.1417-13.31932.3227
50.0026-0.00060.0005-0.0010.00230.0023-0.11210.03780.0105-0.0767-0.0487-0.0512-0.05420.1205-0.09320.1551-0.17180.02890.25410.21430.216350.0039-24.792-5.4419
60.00540.001-0.0023-0.0007-0.00330.0075-0.0981-0.01770.02670.0026-0.0135-0.0208-0.0299-0.1392-0.02060.12180.02820.03280.222-0.08320.212842.0479-25.5259-3.8978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 4 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 4 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 4 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 4 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 4 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 4 )

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