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Yorodumi- PDB-1i3t: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i3t | ||||||||||||||||||
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Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATSON-CRICK TYPE AND WOBBLE N4-METHOXYCYTIDINE/GUANOSINE BASE PAIRS IN B-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / N4-METHOXYCYTOSINE / DAMAGED DNA / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Hossain, M.T. / Hikima, T. / Chatake, T. / Masaru, T. / Sunami, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. | Citation | Journal: J.Biochem.(Tokyo) / Year: 2001 | Title: Crystallographic studies on damaged DNAs: III. N(4)-methoxycytosine can form both Watson-Crick type and wobbled base pairs in a B-form duplex. Authors: Hossain, M.T. / Chatake, T. / Hikima, T. / Tsunoda, M. / Sunami, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i3t.cif.gz | 26.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i3t.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i3t ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i3t | HTTPS FTP |
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-Related structure data
Related structure data | 1i47C 355dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, magnesium acetate, spermine, sodium cacodylate. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277 K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.6→100 Å / Num. all: 9068 / Num. obs: 9068 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.08 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique all: 759 / % possible all: 93.9 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 100 Å / Rmerge(I) obs: 0.08 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 355D Resolution: 1.6→10 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10.5 % / Rfactor obs: 0.224 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.429 / % reflection Rfree: 8.9 % / Rfactor Rwork: 0.376 |