[English] 日本語
Yorodumi- PDB-5bna: THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bna | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-G-C-G-A-A-T-T-C-G-C-G | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | PLATINUM TRIAMINE ION / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | Authors | Wing, R.M. / Pjura, P. / Drew, H.R. / Dickerson, R.E. | Citation | Journal: EMBO J. / Year: 1984 Title: The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G Authors: Wing, R.M. / Pjura, P. / Drew, H.R. / Dickerson, R.E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: A Random-Walk Model for Helix Bending in B-DNA Authors: Dickerson, R.E. / Kopka, M.L. / Pjura, P. #2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1983 Title: Helix Geometry and Hydration in A-DNA, B-DNA and Z-DNA Authors: Dickerson, R.E. / Drew, H.R. / Conner, B.N. / Kopka, M.L. / Pjura, P.E. #3: Journal: Biological Macromolecules and Assemblies / Year: 1985 Title: Base Sequence, Helix Geometry, Hydration and Helix Stability in B-DNA Authors: Dickerson, R.E. / Kopka, M.L. / Pjura, P. #4: Journal: Nature / Year: 1980 Title: Crystal Structure Analysis of a Complete Turn of B-DNA Authors: Wing, R. / Drew, H.R. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5bna.cif.gz | 28.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5bna.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 5bna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/5bna ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bna | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: THE ANISOTROPIC TEMPERATURE FACTORS FOR THE PLATINUM ATOMS ARE AS FOLLOWS ATOM B11 B22 B33 B12 B13 B23 PT1 PTN 25 0.01510 0.00438 0.00138 0.00214 0.00056 0.00026 PT1 PTN 26 0.01545 0.00544 0.00131- ...1: THE ANISOTROPIC TEMPERATURE FACTORS FOR THE PLATINUM ATOMS ARE AS FOLLOWS ATOM B11 B22 B33 B12 B13 B23 PT1 PTN 25 0.01510 0.00438 0.00138 0.00214 0.00056 0.00026 PT1 PTN 26 0.01545 0.00544 0.00131-0.00462-0.00072 0.00017 PT1 PTN 27 0.00729 0.00382 0.00120-0.00092-0.00060 0.00039 2: TEMPERATURE FACTORS WHICH WERE CALCULATED TO BE NON-POSITIVE-DEFINITE WERE ARBITRARILY SET TO 0.0 IN THE REFINEMENT PROCEDURE. |
-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.49 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K | |||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||
Crystal grow | *PLUS Details: Wing, R., (1980) Nature, 287, 755. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | Highest resolution: 2.6 Å / Num. obs: 2088 |
---|
-Processing
Software | Name: JACK-LEVITT / Classification: refinement | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.6→8 Å / σ(F): 2 /
| ||||||||||||||||
Refine Biso |
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
| ||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Num. reflection all: 2012 / σ(F): 2 / Rfactor all: 0.166 / Rfactor obs: 0.112 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |