+Open data
-Basic information
Entry | Database: PDB / ID: 6a1q | ||||||
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Title | Crystal structures of disordered Z-type helices | ||||||
Components |
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Keywords | DNA / Tetradecamer sequence / alternate pyr-pur repeat / left handed Z-DNA duplex / discontinuous helices / P3(2) | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å | ||||||
Authors | Karthik, S. / Mandal, P.K. / Thirugnanasambandam, A. / Gautham, N. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a1q.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a1q.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 6a1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/6a1q ftp://data.pdbj.org/pub/pdb/validation_reports/a1/6a1q | HTTPS FTP |
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-Related structure data
Related structure data | 6a1oC 3p4jS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.2546760 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1221.840 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 1159.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density 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. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50mM sodium cacodylate trihydrate buffer, 200mM MgSO4, 50% MPD. |
-Data collection
Diffraction | Mean temperature: 293 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,-k,l / Fraction: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method 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.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→16.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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