[English] 日本語
Yorodumi- PDB-1zjm: Human DNA Polymerase beta complexed with DNA containing an A-A mi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zjm | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus | ||||||
Components |
| ||||||
Keywords | DNA/LYASE/TRANSFERASE / NUCLEOTIDYLTRANSFERASE / DNA REPAIR / DNA MISMATCH / BASE EXCISION REPAIR / DNA-LYASE-TRANSFERASE 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 / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair ...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 / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Batra, V.K. / Beard, W.A. / Shock, D.D. / Pedersen, L.C. / Wilson, S.H. | ||||||
Citation | Journal: STRUCTURE / Year: 2005 Title: Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Authors: Batra, V.K. / Beard, W.A. / Shock, D.D. / Pedersen, L.C. / Wilson, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zjm.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zjm.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zjm ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zjm | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zjnC 1bpxS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4813.134 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 3085.029 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 / Production host: Escherichia coli (E. coli) References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
---|
-Non-polymers , 2 types, 347 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350, Sodium Acetate, Imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2003 |
Radiation | Monochromator: Osmic Mirrors / 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: 25752 / Num. obs: 24584 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.436 / % possible all: 92.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BPX Resolution: 2.1→30.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 259227.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5242 Å2 / ksol: 0.323422 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|