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- PDB-1nkc: A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-TH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nkc | |||||||||
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Title | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | |||||||||
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![]() | Transferase/DNA / DNA POLYMERASE I / DNA REPLICATION / KLENOW FRAGMENT / PROTEIN-DNA COMPLEX / DNA MISMATCH / Transferase-DNA COMPLEX | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Johnson, S.J. / Beese, L.S. | |||||||||
![]() | ![]() Title: Structures of mismatch replication errors observed in a DNA polymerase. Authors: Johnson, S.J. / Beese, L.S. #1: ![]() 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. #2: ![]() Title: Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal Authors: Kiefer, J.R. / Mao, C. / Braman, J.C. / Beese, L.S. #3: ![]() Title: Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 A Resolution Authors: Kiefer, J.R. / Mao, C. / Hansen, C.J. / Basehore, S.L. / Hogrefe, H.H. / Braman, J.C. / Beese, L.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.6 KB | Display | ![]() |
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PDB format | ![]() | 122.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 876.7 KB | Display | ![]() |
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Full document | ![]() | 881.8 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1njwC ![]() 1njxC ![]() 1njyC ![]() 1njzC ![]() 1nk0C ![]() 1nk4C ![]() 1nk5C ![]() 1nk6C ![]() 1nk7C ![]() 1nk8C ![]() 1nk9C ![]() 1nkbC ![]() 1nkeC ![]() 2bdpS C: citing same article ( S: Starting model for refinement |
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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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Details | Exists as a monomer. One molecule per asymmetric unit. |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 4594.986 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4600.983 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein / Sugars , 2 types, 2 molecules A
#3: Protein | Mass: 66172.844 Da / Num. of mol.: 1 Fragment: BACILLUS FRAGMENT (ANALOGOUS TO THE E. COLI KLENOW FRAGMENT) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET-30A(+) / Production host: ![]() ![]() |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
-Non-polymers , 3 types, 617 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THE POLYMERASE ADOPTS AN OPEN CONFORMATION WITH A GUANINE-THYMINE MISMATCH BOUND AT THE N-6 ...THE POLYMERASE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 5.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 5.8 / Method: vapor diffusion, hanging dropDetails: Johnson, S.J., (2003) Proc.Natl.Acad.Sci.USA, 100, 3895. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 1998 / Details: MIRRORS |
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: 1.8→26.76 Å / Num. all: 62356 / Num. obs: 62356 / % possible obs: 76.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 31.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 1345 / Rsym value: 0.136 / % possible all: 16.8 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Num. measured all: 209950 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Rmerge(I) obs: 0.136 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BDP Resolution: 1.8→26.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2096283.71 / Data cutoff high rms absF: 2096283.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: THE BACILLUS POLYMERASE WAS CO- CRYSTALLIZED WITH A DNA CONTAINING A 10 BASE PAIR DUPLEX AND A 5 BASE 5' TEMPLATE OVERHANG. THE CRYSTAL WAS SUBSEQUENTLY PLACED INTO A STABILIZING SOLUTION ...Details: THE BACILLUS POLYMERASE WAS CO- CRYSTALLIZED WITH A DNA CONTAINING A 10 BASE PAIR DUPLEX AND A 5 BASE 5' TEMPLATE OVERHANG. THE CRYSTAL WAS SUBSEQUENTLY PLACED INTO A STABILIZING SOLUTION CONTAINING DCTP, DGTP, DTTP, AND DATP. THE RESULTING PRODUCT COMPLEX CONTAINED 15 BASE PAIRS OF DUPLEX DNA. A 3' PHOSPHATE WAS LOCATED ON THE TEMPLATE STRAND (CHAIN C) TO ENSURE THAT THE DNA DUPLEX WAS NOT BOUND BACKWARDS BY THE POLYMERASE DURING CRYSTALLIZATION. ELECTRON DENSITY WAS OBSERVED FOR ALL PROTEIN SIDE CHAINS EXCEPT LYSINE 298, WHICH WAS MODELLED TO THE BETA CARBON. 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: 43.2757 Å2 / ksol: 0.391199 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→26.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.23 |