+Open data
-Basic information
Entry | Database: PDB / ID: 1ue4 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of d(GCGAAAGC) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / sheared G:A pair / bulge-in duplex / G:AxA:G crossing | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | Authors | Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 | Title: Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing. Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ue4.cif.gz | 15 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ue4.ent.gz | 9.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ue4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/1ue4 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/1ue4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ub8C 1ue2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 2460.644 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 19.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium chloride, magnesium chloride, spermine 4HCl, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / 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: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2001 |
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→26 Å / Num. all: 3177 / Num. obs: 3175 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 88780 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 100 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UE2 Resolution: 1.65→15 Å / σ(F): 3 Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.71 Å /
| ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|