[English] 日本語
Yorodumi- PDB-1g75: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG): 5-FORMYLURI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g75 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG): 5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / MODIFIED NUCLEOTIDE / FORMYLURIDINE / DNA DAMAGE / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | Function / homology | : / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | Authors | Tsunoda, M. / Karino, N. / Ueno, Y. / Matsuda, A. / Takenaka, A. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 | Title: Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers? Authors: Tsunoda, M. / Karino, N. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g75.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g75.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g75_validation.pdf.gz | 321.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1g75_full_validation.pdf.gz | 321.3 KB | Display | |
Data in XML | 1g75_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 1g75_validation.cif.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g75 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g75 | HTTPS FTP |
-Related structure data
Related structure data | 1g8nC 1g8uC 1g8vC 355dS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3677.376 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-K / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, spermine, magnesium chloride, potassium chloride, sodium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. all: 90663 / Num. obs: 9502 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 9.54 % / Rmerge(I) obs: 0.031 |
Reflection shell | Resolution: 1.57→1.6 Å / Rmerge(I) obs: 0.266 / % possible all: 89.9 |
Reflection | *PLUS Num. measured all: 90663 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 355D Resolution: 1.57→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||
Refine analyze |
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→50 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
LS refinement shell | Resolution: 1.57→1.67 Å / Rfactor Rfree error: 0.021 /
| ||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 / % reflection Rfree: 10 % | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.263 / Rfactor Rwork: 0.235 |