+Open data
-Basic information
Entry | Database: PDB / ID: 1u4b | |||||||||
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Title | Extension of an adenine-8oxoguanine mismatch | |||||||||
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 double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 1u4b.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u4b.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 1u4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u4b_validation.pdf.gz | 894.4 KB | Display | wwPDB validaton report |
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Full document | 1u4b_full_validation.pdf.gz | 903.5 KB | Display | |
Data in XML | 1u4b_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 1u4b_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u4b ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u4b | HTTPS FTP |
-Related structure data
Related structure data | 1u45C 1u47C 1u48C 1u49C 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: 3951.586 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, 596 molecules
#5: Chemical | ChemComp-SO4 / #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: 2.66 Å3/Da / Density % sol: 53.5 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Ammonium Sulfate, Magnesium Sulfate, MPD, MES, pH 5.8, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2004 Details: Elliptically bent mirror/sagittal focusing second monochromator crystal |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→40.75 Å / Num. all: 114192 / Num. obs: 114192 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1L3S Resolution: 1.6→40.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 355920.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The magnesium 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 magnesium 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: 44.5119 Å2 / ksol: 0.396565 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→40.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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