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Yorodumi- PDB-2ajq: Structure of replicative DNA polymerase provides insigts into the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ajq | ||||||
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Title | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing | ||||||
Components |
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Keywords | TRANSFERASE / TRANSCRIPTION/DNA / Polymerase T7 / x-ray crystallography / ternary complex / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication ...DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Enterobacteria phage T7 (virus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Brieba, L. / Ellenberger, T. | ||||||
Citation | Journal: To be Published Title: Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing Authors: Brieba, L. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ajq.cif.gz | 375.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ajq.ent.gz | 299.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ajq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ajq_validation.pdf.gz | 497.5 KB | Display | wwPDB validaton report |
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Full document | 2ajq_full_validation.pdf.gz | 555.2 KB | Display | |
Data in XML | 2ajq_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 2ajq_validation.cif.gz | 96.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/2ajq ftp://data.pdbj.org/pub/pdb/validation_reports/aj/2ajq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6739.384 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 8026.148 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 79703.578 Da / Num. of mol.: 2 / Mutation: Residues 5 and 7 mutated to Ala Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses Description: Protein induced at an OD_600 of 0.5 by addition of 0.5 mM IPTG for 4 hours at 37C Gene: 5 / Plasmid: pGP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys S / References: UniProt: P00581, DNA-directed DNA polymerase #4: Protein | Mass: 11687.388 Da / Num. of mol.: 2 / Mutation: Residues 5 and 7 mutated to Ala Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: Protein induced at an OD_600 of 0.5 by addition of 0.5 mM IPTG for 4 hours at 37C Gene: trxA, fipA, tsnC / Plasmid: p-Trx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys S / References: UniProt: P0AA25 #5: 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: 3.18 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: A complex of 1x10^-4 M T7 DNA polymerase 5A7A:thioredoxin was assembled with an equimolar amount of double stranded DNA substrate. Crystallization was achieved using a buffer containing 50mM ...Details: A complex of 1x10^-4 M T7 DNA polymerase 5A7A:thioredoxin was assembled with an equimolar amount of double stranded DNA substrate. Crystallization was achieved using a buffer containing 50mM HEPES pH 7.5, 10mM MgCl_2, 2mM DTT, and 0.5 mM terminal ddTTP Seed crystals were grown by hanging drop vapor diffusion by mixing 1ul each of protein-DNA solution and a reservoir solutions containing between 16 to 20% PEG 8000, 100mM ACES pH 7.5, 120 ammonium sulfate, 30mM MgCl2, and 5mM DTT. These crystals were used to streak-seed a grid of protein/reservoir solutions with concentrations of PEG 8000 between 13 to 15%. Pyramidal crystals appeared overnight and reached a maximum size of ~150 X 150 X 100 um3 after 3 to 4 days. Crystals were harvested overnight in mother-liquor containing 10 % PEG 400, temperature 273K, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2005 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→45.97 Å / Num. all: 98459 / Num. obs: 76808 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.111 / Net I/σ(I): 16.8 |
Reflection shell | Highest resolution: 2.38 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4557696.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.0629 Å2 / ksol: 0.315331 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→45.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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