[English] 日本語
![](img/lk-miru.gif)
- PDB-2w9b: Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine mod... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2w9b | ||||||
---|---|---|---|---|---|---|---|
Title | Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / N2-DIMETHYL-G / METAL-BINDING / MUTATOR PROTEIN / DNA DAMAGE / DNA REPAIR / DNA-BINDING / TRANSFERASE / DNA REPLICATION / NUCLEOTIDYLTRANSFERASE / DNA / DPO4 / ADDUCT / CYTOPLASM / MAGNESIUM / POLYMERASE / TRANSFERASE-DNA complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Eoff, R.L. / Zhang, H. / Kosekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. | ||||||
![]() | ![]() Title: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. Authors: Zhang, H. / Eoff, R.L. / Kosekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 148 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 606 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 63.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w9aC ![]() 2w9cC ![]() 2asdS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-DNA POLYMERASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 41114.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 41086.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 4 molecules CDEF
#3: DNA chain | Mass: 4369.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT C(DOC) -3' #4: DNA chain | Mass: 5415.545 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: 18 BASE TEMPLATE DNA 5'-TCA T(M2G)G AAT CCT TCC CCC-3' |
---|
-Non-polymers , 2 types, 207 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 53.21 % / Description: NONE |
---|---|
Crystal grow | pH: 7.4 Details: DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 1 MM DGTP. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→28.75 Å / Num. obs: 45625 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.28→2.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.8 / % possible all: 89.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ASD Resolution: 2.28→28.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114169.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.7 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→28.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|