+Open data
-Basic information
Entry | Database: PDB / ID: 4kll | ||||||
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Title | DNA polymerase beta matched product complex with Mg2+, 45 min | ||||||
Components |
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Keywords | TRANSFERASE / LYASE/DNA / DNA polymerase / LYASE-DNA complex | ||||||
Function / homology | Function and homology information Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / salivary gland morphogenesis / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / salivary gland morphogenesis / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.841 Å | ||||||
Authors | Freudenthal, B.D. / Beard, W.A. / Shock, D.D. / Wilson, S.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: Observing a DNA polymerase choose right from wrong. Authors: Freudenthal, B.D. / Beard, W.A. / Shock, D.D. / Wilson, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kll.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kll.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 4kll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kll_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 4kll_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 4kll_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4kll_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/4kll ftp://data.pdbj.org/pub/pdb/validation_reports/kl/4kll | HTTPS FTP |
-Related structure data
Related structure data | 4kldC 4kleC 4klfC 4klgC 4klhC 4kliC 4kljC 4klmC 4kloC 4klqC 4klsC 4kltC 4kluC 4lvsC 2fmsS 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 , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Polb / Plasmid: pWL11 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56 References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 5 types, 345 molecules
#5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-PPV / | #7: Chemical | ChemComp-MG / | #8: Chemical | #9: 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: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 29, 2012 / Details: mirrors |
Diffraction measurement | Details: 0.25 degrees, 45.0 sec, detector distance 50.00 mm |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.061 / Number: 93621 |
Reflection | Resolution: 1.841→50 Å / Num. all: 93621 / Num. obs: 33832 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1.124 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.841→1.92 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.363 / Rsym value: 0.297 / % possible all: 80.9 |
Cell measurement | Reflection used: 93621 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FMS Resolution: 1.841→23.758 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8156 / SU ML: 0.25 / σ(F): 0 / Phase error: 25.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.837 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.55 Å2 / Biso mean: 31.0714 Å2 / Biso min: 12.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.841→23.758 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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