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Yorodumi- PDB-3k57: Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k57 | ||||||
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Title | Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / SOS response / Transferase / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Yang, W. / Wang, F. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: Structural insight into translesion synthesis by DNA Pol II Authors: Wang, F. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k57.cif.gz | 203.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k57.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k57 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k57 | HTTPS FTP |
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-Related structure data
Related structure data | 3k58C 3k59C 3k5lC 3k5mC 3k5nC 3k5oC 3maqC 1q8iS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 90459.734 Da / Num. of mol.: 1 / Mutation: D335N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0060, dinA, JW0059, polB Plasmid: Modified PET28 with prescission protease cleavage site Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21189, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis |
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#3: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis |
-Non-polymers , 3 types, 528 molecules
#4: Chemical | ChemComp-DTP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 20% PEGmme5000, 0.2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→20 Å / Num. all: 61590 / Num. obs: 57617 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6065 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q8I Resolution: 2.08→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.15 Å
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