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Yorodumi- PDB-1nom: DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nom | |||||||||
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Title | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) | |||||||||
Components | DNA POLYMERASE BETA | |||||||||
Keywords | NUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR | |||||||||
Function / homology | Function and homology information Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / 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) lyase / spindle microtubule / response to gamma radiation / base-excision repair / 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 / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å | |||||||||
Authors | Pelletier, H. / Sawaya, M.R. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Authors: Pelletier, H. / Sawaya, M.R. #1: Journal: To be Published Title: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates Authors: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H. #2: Journal: To be Published Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity Authors: Pelletier, H. #3: Journal: Biochemistry / Year: 1996 Title: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #4: Journal: Biochemistry / Year: 1996 Title: A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #5: Journal: Biochemistry / Year: 1996 Title: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis Authors: Pelletier, H. / Sawaya, M.R. #7: Journal: Science / Year: 1994 Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template-Primer, and ddCTP Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. #8: Journal: Science / Year: 1994 Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nom.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nom.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1nom ftp://data.pdbj.org/pub/pdb/validation_reports/no/1nom | HTTPS FTP |
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-Related structure data
Related structure data | 1zqaC 1zqbC 1zqcC 1zqdC 1zqeC 1zqfC 1zqgC 1zqhC 1zqiC 1zqjC 1zqkC 1zqlC 1zqmC 1zqnC 1zqoC 1zqpC 1zqqC 1zqrC 1zqsC 1zquC 1zqvC 1zqwC 1zqxC 1zqyC 1zqzC 8icaC 8icbC 8iccC 8iceC 8icfC 8icgC 8ichC 8iciC 8iczC 9icaC 9icbC 9iccC 9iceC 9icgC 9ichC 9iciC 9icjC 9iclC 1bpbS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28774.527 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335) Source method: isolated from a genetically manipulated source Details: SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: POL / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
Compound details | PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN (RESIDUES 88 - 335) AND THE N-TERMINAL 8 KD ...PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN (RESIDUES 88 - 335) AND THE N-TERMINAL 8 KD DOMAIN IS NOT PRESENT IN THIS STRUCTURE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 1 MONTH: PEG 1500, 15% HEPES, 75 MILLIMOLAR, PH 7.5 NACL, 50 MILLIMOLAR DTT, 0.1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.5 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 17, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 6027 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.064 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.166 / % possible all: 92 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.166 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1BPB Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS AND KRETSINGER (STANDARD TNT) / Bsol: 381 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5-D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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