+Open data
-Basic information
Entry | Database: PDB / ID: 3bdp | ||||||
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Title | DNA POLYMERASE I/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSFERASE/DNA / BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE / BF THERMOPHILUS POLYMERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA) / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kiefer, J.R. / Mao, C. / Beese, L.S. | ||||||
Citation | 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. #1: Journal: Structure / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bdp.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bdp.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bdp_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 3bdp_full_validation.pdf.gz | 488.9 KB | Display | |
Data in XML | 3bdp_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 3bdp_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/3bdp ftp://data.pdbj.org/pub/pdb/validation_reports/bd/3bdp | HTTPS FTP |
-Related structure data
Related structure data | 2bdpSC 4bdpC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: DNA chain | Mass: 3044.017 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 3029.006 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 66200.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P52026, DNA-directed DNA polymerase | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % Description: LTI/SIGMA(I)> FOR THE DATA SET : 26.4 LTI/SIGMA(I)> FOR SHELL : 6.1 | ||||||||||||||||||||||||||||||
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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 dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 63997 / Num. obs: 63997 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.061 |
Reflection shell | Resolution: 1.9→1.93 Å / Rsym value: 0.187 / % possible all: 75.4 |
Reflection | *PLUS Num. measured all: 326641 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 75.4 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BDP Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.389 |