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Yorodumi- PDB-7atg: Crystal structure of Z-DNA in complex with putrescinium and potas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7atg | ||||||||||||||||||||||||||||
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Title | Crystal structure of Z-DNA in complex with putrescinium and potassium cations at ultrahigh-resolution | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / dual-conformation backbone / putrescinium cation / biogenic polyamines / potassium complex | Function / homology | 4-azaniumylbutylazanium / : / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.6 Å | Authors | Drozdzal, P. / Gilski, M. / Jaskolski, M. | Funding support | Poland, 1items |
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 2021 | Title: Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution. Authors: Drozdzal, P. / Gilski, M. / Jaskolski, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7atg.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7atg.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 7atg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7atg_validation.pdf.gz | 761.8 KB | Display | wwPDB validaton report |
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Full document | 7atg_full_validation.pdf.gz | 761.7 KB | Display | |
Data in XML | 7atg_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 7atg_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7atg ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atg | HTTPS FTP |
-Related structure data
Related structure data | 4higS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m37atg / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / | #3: Chemical | ChemComp-58I / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.8 Å3/Da / Density % sol: 31.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%(v/v) (+/-)-2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM NaCl, 14 mM putrescinium dichloride |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 0.6→25.33 Å / Num. obs: 107989 / % possible obs: 90.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 5.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.024 / Rrim(I) all: 0.027 / Χ2: 1.143 / Net I/σ(I): 29.84 | ||||||||||||||||||
Reflection shell | Resolution: 0.6→0.61 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 1973 / CC1/2: 0.999 / Rrim(I) all: 0.368 / % possible all: 22.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4hig Resolution: 0.6→25.33 Å / Num. parameters: 3962 / Num. restraintsaints: 4374 / Cross valid method: FREE R-VALUE Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES PROCEDURE. CONFORMATION-DEPENDENT GEOMETRICAL RESTRAINTS ON BOND LENGTHS AND BOND ANGLES FOR POLYNUCLEOTIDE CHAINS WERE GENERATED USING THE RESTRAINTLIB SERVER: http://achesym.ibch.poznan.pl/restraintlib/
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 36.87 Å2 / Biso mean: 6.26 Å2 / Biso min: 2.73 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 141.29 / Occupancy sum non hydrogen: 333.73 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.6→25.33 Å
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Refine LS restraints |
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