[English] 日本語
![](img/lk-miru.gif)
- PDB-8scm: Bst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-am... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8scm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-amino primer, dGTP, and calcium time-resolved 8h | |||||||||
![]() |
| |||||||||
![]() | REPLICATION/DNA / DNA Polymerase / NP-DNA / Origin of Life / Time-Resolved Crystallography / REPLICATION-DNA complex | |||||||||
Function / homology | ![]() double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fang, Z. / Lelyveld, V.S. / Szostak, J.W. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity. Authors: Lelyveld, V.S. / Fang, Z. / Szostak, J.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 339.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 215.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8scgC ![]() 8sciC ![]() 8scjC ![]() 8sckC ![]() 8sclC ![]() 8scnC ![]() 8scoC ![]() 8scpC ![]() 8scqC ![]() 8scrC ![]() 8scsC ![]() 8sctC ![]() 8scuC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 66073.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DPO1, polA / Production host: ![]() ![]() |
---|
-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 3069.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3936.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Non-polymers , 5 types, 227 molecules ![](data/chem/img/DPO.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.35 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2M ammonium sulphate, 0.1M MES pH 5.3-6.0, 20 mM CaCl2, 5% MPD PH range: 5.3-6.0 |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 67705 / % possible obs: 97.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.92 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Χ2: 0.863 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3 / Num. unique obs: 3421 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.266 / Rrim(I) all: 0.567 / Χ2: 0.783 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|