[English] 日本語
![](img/lk-miru.gif)
- PDB-4xiu: Binary complex structure of Klenow fragment of Taq DNA polymerase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xiu | ||||||
---|---|---|---|---|---|---|---|
Title | Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / protein-DNA complex / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wu, E.Y. | ||||||
![]() | ![]() Title: A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Authors: Wu, E.Y. / Walsh, A.R. / Materne, E.C. / Hiltner, E.P. / Zielinski, B. / Miller, B.R. / Mawby, L. / Modeste, E. / Parish, C.A. / Barnes, W.M. / Kermekchiev, M.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 137.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n56C ![]() 4n5sC ![]() 4ktqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is the same as asym. |
-
Components
#1: DNA chain | Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 4328.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 60865.887 Da / Num. of mol.: 1 Fragment: Klenow fragment of DNA polymerase I from Thermus aquatics Mutation: I707L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 21497 / Num. obs: 21497 / % possible obs: 96.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Χ2: 2.684 / Net I/av σ(I): 21.394 / Net I/σ(I): 11.55 / Num. measured all: 102057 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.96 % / Num. unique all: 1322 / Χ2: 3.7 / Rejects: 0 / % possible all: 97.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4KTQ Resolution: 2.5→47.64 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2965 / WRfactor Rwork: 0.2231 / FOM work R set: 0.777 / SU B: 12.317 / SU ML: 0.27 / SU R Cruickshank DPI: 1.0086 / SU Rfree: 0.3542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.009 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.39 Å2 / Biso mean: 52.506 Å2 / Biso min: 22.05 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|