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- PDB-1xwl: BACILLUS STEAROTHERMOPHILUS (NEWLY IDENTIFIED STRAIN AS YET UNNAM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xwl | |||||||||
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Title | BACILLUS STEAROTHERMOPHILUS (NEWLY IDENTIFIED STRAIN AS YET UNNAMED) DNA POLYMERASE FRAGMENT | |||||||||
![]() | DNA POLYMERASE I | |||||||||
![]() | DNA REPLICATION / BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE / BF THERMOPHILUS POLYMERASE | |||||||||
Function / homology | ![]() 5'-3' exonuclease activity / 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 | ![]() ![]() | |||||||||
![]() | Kiefer, J.R. / Mao, C. / Beese, L.S. | |||||||||
![]() | ![]() 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.1 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bdp 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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Components
#1: Protein | Mass: 66172.844 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | BACILLUS FRAGMENT (BF) IS THE C-TERMINAL 592 AMINO ACIDS OF THE WILD TYPE BACILLUS DNA POLYMERASE. ...BACILLUS FRAGMENT (BF) IS THE C-TERMINAL 592 AMINO ACIDS OF THE WILD TYPE BACILLUS DNA POLYMERASE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 63.4 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 89072 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.038 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.182 / % possible all: 83.1 |
Reflection | *PLUS Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 83.1 % / Rmerge(I) obs: 0.182 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ORIGINAL 1BDP COORDINATES ![]() 1bdp Resolution: 1.7→20 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016
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Xplor file |
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