[English] 日本語
![](img/lk-miru.gif)
- PDB-1d5a: CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEP... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d5a | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM | ||||||
![]() | PROTEIN (DNA POLYMERASE) | ||||||
![]() | TRANSFERASE / DNA POLYMERASE / THERMOSTABLE / EXONUCLEASE / RBD DOMAIN | ||||||
Function / homology | ![]() exonuclease activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding ...exonuclease activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhao, Y. / Jeruzalmi, D. / Leighton, L. / Lasken, R. / Kuriyan, J. | ||||||
![]() | ![]() Title: Crystal structure of an archaebacterial DNA polymerase. Authors: Zhao, Y. / Jeruzalmi, D. / Moarefi, I. / Leighton, L. / Lasken, R. / Kuriyan, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 410.9 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 84905.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7SIG8, UniProt: Q7SIG7*PLUS, DNA-directed DNA polymerase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 42684 / Num. obs: 37229 / % possible obs: 87.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→50 Å / Redundancy: 0.5 % / Rmerge(I) obs: 0.319 / Num. unique all: 2313 / % possible all: 53.8 |
Reflection | *PLUS % possible obs: 92.2 % |
Reflection shell | *PLUS % possible obs: 53.8 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |