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Yorodumi- PDB-3k5l: Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) terna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k5l | ||||||
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Title | Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / SOS response / Transferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information 3'-5'-DNA exonuclease activity / DNA replication proofreading / 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: 2.7 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 | 3k5l.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k5l.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 3k5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k5l_validation.pdf.gz | 805.9 KB | Display | wwPDB validaton report |
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Full document | 3k5l_full_validation.pdf.gz | 842.9 KB | Display | |
Data in XML | 3k5l_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 3k5l_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k5l ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k5l | HTTPS FTP |
-Related structure data
Related structure data | 3k57SC 3k58C 3k59C 3k5mC 3k5nC 3k5oC 3maqC S: Starting model for refinement C: citing same article (ref.) |
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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 / 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: 5391.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Abasic template |
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#3: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer |
-Non-polymers , 3 types, 78 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: 2.47 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEGMME3350, 0.2 M ammonium formate, 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: Jun 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 27533 / Num. obs: 24052 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2723 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K57 Resolution: 2.7→22.42 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 12.104 Å2 | ||||||||||||||||||
Displacement parameters | Biso max: 85.93 Å2 / Biso mean: 22.389 Å2 / Biso min: 1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→22.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å /
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