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Yorodumi- PDB-3upq: Crystal structure of the pre-catalytic ternary complex of polymer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3upq | ||||||
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Title | Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T. | ||||||
Components |
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Keywords | TRANSFERASE / LYASE/DNA / DNA / Polymerase / DNA polymerase lambda / ribonucleotide incorporation / LYASE-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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Gosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda Authors: Gosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3upq.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3upq.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 3upq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3upq_validation.pdf.gz | 801.9 KB | Display | wwPDB validaton report |
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Full document | 3upq_full_validation.pdf.gz | 805.3 KB | Display | |
Data in XML | 3upq_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3upq_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/3upq ftp://data.pdbj.org/pub/pdb/validation_reports/up/3upq | HTTPS FTP |
-Related structure data
Related structure data | 3uq0C 3uq2C 4fo6C 3mgiS 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: 36736.039 Da / Num. of mol.: 1 / Fragment: Loop mutant of DNA polymerase lambda / Mutation: SQEENGQQQ to KGET Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / 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 , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 264 molecules A
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | ChemComp-SO4 / #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH RESIDUES SQEENGQQQ IN THE WILDTYPE ...AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTI |
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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: 57.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 37285 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.058 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.357 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MGI Resolution: 1.95→27.444 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.188 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→27.444 Å
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Refine LS restraints |
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LS refinement shell |
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