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- PDB-2bqu: DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bqu | ||||||
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Title | DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine | ||||||
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![]() | TRANSFERASE / P2 DNA POLYMERASE IV / 1N2-ETHENOGUANINE ADDUCT / TRANSLESION DNA POLYMERASE / DDATP / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | ![]() error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Irimia, A. / Loukachevitch, L.V. / Egli, M. | ||||||
![]() | ![]() Title: DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine. Authors: Zang, H. / Goodenough, A.K. / Choi, J.Y. / Irimia, A. / Loukachevitch, L.V. / Kozekov, I.D. / Angel, K.C. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bq3SC ![]() 2bqrC ![]() 2br0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41086.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13-MER DNA PRIMER |
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#3: DNA chain | Mass: 5411.514 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 18-MER TEMPLATE CONTAINING 1, N2-ETHENOGUANINE ADDUCT |
-Non-polymers , 3 types, 120 molecules ![](data/chem/img/DAD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DAD / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 % Description: THE PDB WITH ACCESSION CODE 2BQ3 SERVED AS STARTING MODEL. THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT. |
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Crystal grow | pH: 7 Details: 16% PEG 3350, 0.1 M HEPES PH 7.0, 100 MM CALCIUM ACETATE, 2.5% GLYCEROL, 0.5 MM DDATP, 2.5 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MAR300 / Detector: IMAGE PLATE / Date: Oct 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.25 Å / Num. obs: 17022 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.5→2.66 Å / % possible all: 73.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BQ3 Resolution: 2.5→42.25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 949887.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FIRST NUCLEOTIDE OF THE TEMPLATE DNA IS NOT OBSERVED IN THE STRUCTURE.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8826 Å2 / ksol: 0.314206 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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