[English] 日本語
![](img/lk-miru.gif)
- PDB-1hzs: Crystal structure of a peptide nucleic acid duplex (BT-PNA) conta... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1hzs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a peptide nucleic acid duplex (BT-PNA) containing a bicyclic analogue of thymine | |||||||||
![]() | PEPTIDE NUCLEIC ACID | |||||||||
![]() | PEPTIDE NUCLEIC ACID / double helix / nucleobase analogue / P-form helix / left-handed / right-handed | |||||||||
Function / homology | DNA![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Eldrup, A.B. / Nielsen, B.B. / Haaima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E. | |||||||||
![]() | Journal: Eur.J.Org.Chem. / Year: 2001 Title: 1,8-Naphthyridin-2(1H)-ones. Novel Bicyclic and Tricyclic Analogues of Thymine in Peptide Nucleic Acids (PNAs) Authors: Eldrup, A.B. / Nielsen, B.B. / Haaima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E. #1: ![]() Title: Crystal Structure of a Peptide Nucleic Acid (PNA) Duplex at 1.7 A Resolution Authors: Rasmussen, H. / Kastrup, J.S. / Nielsen, J.N. / Nielsen, J.M. / Nielsen, P.E. #2: ![]() Title: Peptide Nucleic Acids (PNA) Derived from N-(N-methylaminoethyl)glycine. Synthesis, Hybridization and Structural Properties Authors: Haima, G. / Rasmussen, H. / Schmidt, G. / Jensen, D.K. / Kastrup, J.S. / Stafshede, P.W. / Norden, B. / Buchardt, O. / Nielsen, P.E. | |||||||||
History |
| |||||||||
Remark 300 | BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). CHAINS A AND B BUILD A RIGHT-HANDED PNA DOUBLE HELIX AND CHAINS C AND D BUILD A LEFT-HANDED DOUBLE HELIX. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 27.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 20.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pupS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | PNA double helix |
-
Components
#1: DNA chain | Mass: 1733.858 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized as described in the primary reference #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.28 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2-propanol, ammonium sulphate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1999 / Details: segmental toroidal mirror |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→30 Å / Num. all: 6245 / Num. obs: 6233 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.82→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.6 / Num. unique all: 169 / % possible all: 81.6 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PUP Resolution: 1.82→6 Å / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: own target values / Details: OWN PARAMETER AND TOPOLOGY FILE CREATED
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.82→1.9 Å / Total num. of bins used: 8
| |||||||||||||||||||||||||
Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.269 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.266 / % reflection Rfree: 10 % / Rfactor Rwork: 0.241 |