+Open data
-Basic information
Entry | Database: PDB / ID: 5iio | ||||||
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Title | Crystal structure of the DNA polymerase lambda binary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å | ||||||
Authors | Burak, M.J. / Guja, K.E. / Garcia-Diaz, M. | ||||||
Citation | Journal: Embo J. / Year: 2016 Title: A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. Authors: Burak, M.J. / Guja, K.E. / Hambardjieva, E. / Derkunt, B. / Garcia-Diaz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iio.cif.gz | 333.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iio.ent.gz | 272.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iio_validation.pdf.gz | 495.6 KB | Display | wwPDB validaton report |
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Full document | 5iio_full_validation.pdf.gz | 511.5 KB | Display | |
Data in XML | 5iio_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 5iio_validation.cif.gz | 92.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5iio ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5iio | HTTPS FTP |
-Related structure data
Related structure data | 5iiiC 5iijC 5iikC 5iilC 5iimC 5iinC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-DNA chain , 3 types, 12 molecules BFJNCGKODHLP
#1: DNA chain | Mass: 3406.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 1793.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein , 1 types, 4 molecules AEIM
#4: Protein | Mass: 37348.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 2 types, 1219 molecules
#5: Chemical | ChemComp-NA / #6: 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: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→45.09 Å / Num. obs: 118537 / % possible obs: 98.2 % / Redundancy: 6.9 % / Net I/σ(I): 20 |
-Processing
Software |
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Refinement | Resolution: 2.08→45.086 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→45.086 Å
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Refine LS restraints |
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LS refinement shell |
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