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Yorodumi- PDB-4e60: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+60 | ||||||
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Title | Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex | ||||||
Components |
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Keywords | DNA / Z-type DNA double helices / Barium ions | ||||||
Function / homology | : / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Mandal, P.K. / Venkadesh, S. / Gautham, N. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e60.cif.gz | 19.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e60.ent.gz | 12.2 KB | Display | PDB format |
PDBx/mmJSON format | 4e60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e60_validation.pdf.gz | 390.9 KB | Display | wwPDB validaton report |
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Full document | 4e60_full_validation.pdf.gz | 403 KB | Display | |
Data in XML | 4e60_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 4e60_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e60 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e60 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: DNA chain | Mass: 588.441 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-BA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.6512 Å3/Da / Density % sol: 25.5074 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 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: Sep 8, 2008 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 13.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→25.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
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