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Yorodumi- PDB-1u45: 8oxoguanine at the pre-insertion site of the polymerase active site -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u45 | |||||||||
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Title | 8oxoguanine at the pre-insertion site of the polymerase active site | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase I / DNA replication / klenow fragment / protein-DNA complex / 8oxoguanine / DNA lesion / translation replication / TRANSFERASE-DNA COMPLEX | |||||||||
Function / homology | Function and homology information 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | |||||||||
Authors | Hsu, G.W. / Ober, M. / Carell, T. / Beese, L.S. | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Authors: Hsu, G.W. / Ober, M. / Carell, T. / Beese, L.S. #1: Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Structures of Mismatch Replication Errors Observed in a DNA Polymerase Authors: Johnson, S.J. / Beese, L.S. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations Authors: Johnson, S.J. / Taylor, J.S. / Beese, L.S. #3: Journal: Nature / Year: 1998 Title: Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal Authors: Kiefer, J.R. / Mao, C. / Braman, J.C. / Beese, L.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u45.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u45.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 1u45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u45 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u45 | HTTPS FTP |
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-Related structure data
Related structure data | 1u47C 1u48C 1u49C 1u4bC 1l3sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Exists as a monomer. One molecule per asymmetric unit. |
-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3020.979 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4625.997 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein / Sugars , 2 types, 2 molecules A
#3: Protein | Mass: 66114.742 Da / Num. of mol.: 1 / Fragment: analogous to the E. coli klenow fragment Source method: isolated from a genetically manipulated source Details: see remark 400 Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pet-30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: P52026, DNA-directed DNA polymerase |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
-Non-polymers , 3 types, 572 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: Ammonium sulfate, magnesium sulfate, mpd, mes, pH 5.90, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 2003 / Details: double mirror optics |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.09 Å / Num. all: 59226 / Num. obs: 58360 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 6.4 / Num. unique all: 4503 / Rsym value: 0.122 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L3S Resolution: 2.01→41.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2562396.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The magensium at position 920 was assigned due to the low refined b-factor and comparison with a related klentaq polymerase structure (3KTQ). However, the resolution of the structure ...Details: The magensium at position 920 was assigned due to the low refined b-factor and comparison with a related klentaq polymerase structure (3KTQ). However, the resolution of the structure prevents a definitive assignment between water and magnesium.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.8537 Å2 / ksol: 0.389365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→41.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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Xplor file |
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