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Yorodumi- PDB-7m09: Pre-catalytic quaternary complex of DNA Polymerase Lambda with bl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m09 | |||||||||
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Title | Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP | |||||||||
Components |
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Keywords | TRANSFERASE / Nonhomologous end-joining / Base Excision Repair | |||||||||
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 / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Kaminski, A.M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining. Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Bebenek, K. / Kunkel, T.A. / Pedersen, L.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m09.cif.gz | 207.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m09.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 7m09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/7m09 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/7m09 | HTTPS FTP |
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-Related structure data
Related structure data | 7m07C 7m0aC 7m0bC 7m0dC 7m0eC 2pfoS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38550.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 4 types, 4 molecules TPDU
#2: DNA chain | Mass: 1505.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 7 types, 453 molecules
#6: Chemical | ChemComp-DUP / | ||||||||
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#7: Chemical | ChemComp-CA / | ||||||||
#8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 80mM Na cacodylate pH 6.5, 0.16mM calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 57424 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 1 / CC star: 1 / Rsym value: 0.067 / Χ2: 0.523 / Net I/σ(I): 20.57 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2805 / CC1/2: 0.75 / CC star: 0.926 / Rsym value: 0.803 / Χ2: 0.36 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PFO Resolution: 1.65→39.17 Å / SU ML: 0.1766 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8191 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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