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Yorodumi- PDB-1rzt: Crystal structure of DNA polymerase lambda complexed with a two n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzt | ||||||
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Title | Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase lambda / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pedersen, L.C. / Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Blanco, L. / Kunkel, T.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology. Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Blanco, L. / 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 | 1rzt.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzt.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rzt_validation.pdf.gz | 516.5 KB | Display | wwPDB validaton report |
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Full document | 1rzt_full_validation.pdf.gz | 545.8 KB | Display | |
Data in XML | 1rzt_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 1rzt_validation.cif.gz | 91.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzt ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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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Details | biological unit unknown |
-Components
-DNA chain , 3 types, 12 molecules BFJNCGKODHLP
#1: DNA chain | Mass: 3328.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: template DNA #2: DNA chain | Mass: 1536.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: upstream primer DNA #3: DNA chain | Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: downstream primer DNA |
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-Protein , 1 types, 4 molecules AEIM
#4: Protein | Mass: 37052.238 Da / Num. of mol.: 4 / Fragment: catalytic domain of polymerase lambda / Mutation: residues 245-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9UGP5, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 1037 molecules
#5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-EDO / | #7: 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: 2.86 Å3/Da / Density % sol: 56.98 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6 Details: cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 111222 / Num. obs: 111222 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7770 / Rsym value: 0.284 / % possible all: 67.2 |
Reflection | *PLUS Num. measured all: 590501 / Rmerge(I) obs: 0.475 |
Reflection shell | *PLUS % possible obs: 67.2 % / Rmerge(I) obs: 0.284 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polymerase beta Resolution: 2.1→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 557836.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4433 Å2 / ksol: 0.328722 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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