+Open data
-Basic information
Entry | Database: PDB / ID: 3bq1 | ||||||
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Title | Insertion ternary complex of Dbh DNA polymerase | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / Y-family / lesion bypass / single-base deletion / -1 frameshift / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Pata, J.D. / Wilson, R.C. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh. Authors: Wilson, R.C. / Pata, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bq1.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bq1.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bq1_validation.pdf.gz | 853 KB | Display | wwPDB validaton report |
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Full document | 3bq1_full_validation.pdf.gz | 857.8 KB | Display | |
Data in XML | 3bq1_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3bq1_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/3bq1 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bq1 | HTTPS FTP |
-Related structure data
Related structure data | 3bq0C 3bq2C 1im4S 1k1qS 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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-Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 3095.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer |
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#2: DNA chain | Mass: 4472.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 40045.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: dbh / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: Q4JB80, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 43 molecules
#4: Chemical | ChemComp-DG3 / |
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#5: Chemical | ChemComp-CA / |
#6: 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: 2.88 Å3/Da / Density % sol: 57.26 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG-3350, calcium acetate, glycerol, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 15669 / % possible obs: 99.6 % / Observed criterion σ(I): -0.5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1IM4 and 1K1Q Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.757 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.225 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.582 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.786 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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