[English] 日本語
![](img/lk-miru.gif)
- PDB-2xc9: BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2xc9 | ||||||
---|---|---|---|---|---|---|---|
Title | BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | ![]() SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Irimia, A. / Loukachevitch, L.V. / Egli, M. | ||||||
![]() | ![]() Title: Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus Authors: Irimia, A. / Loukachevitch, L.V. / Eoff, R.L. / Guengerich, F.P. / Egli, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xcaC ![]() 2xcpC ![]() 2bq3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41086.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: DNA chain | Mass: 4425.876 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 5396.503 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
Sequence details | THE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED AND MISSING FROM THE STRUCTURE. THE C-TERMINAL 11 ...THE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 48.08 % Description: THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT. |
---|---|
Crystal grow | pH: 7.5 Details: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, AND 20 MM TRIS (PH 7.5) |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2006 Details: ROSENBAUM-ROCK MONOCHROMATOR HIGH -RESOLUTION DOUBLE-CRYSTAL SI (111) SAGITTAL FOCUSING. ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→26.91 Å / Num. obs: 26245 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 12.6 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 6.2 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BQ3 Resolution: 2.2→26.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1362679.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.325 Å2 / ksol: 0.309453 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→26.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|