+Open data
-Basic information
Entry | Database: PDB / ID: 3k5o | ||||||
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Title | Crystal structure of E.coli Pol II | ||||||
Components | DNA polymerase II | ||||||
Keywords | TRANSFERASE / Apo / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / SOS response | ||||||
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: 2.2 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 | 3k5o.cif.gz | 317.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k5o.ent.gz | 256.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k5o ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k5o | HTTPS FTP |
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-Related structure data
Related structure data | 3k57C 3k58C 3k59C 3k5lC 3k5mC 3k5nC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 90459.734 Da / Num. of mol.: 2 / 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 #2: 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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Na Citrate, 10% PEG4000, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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: Nov 15, 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: 2.2→50 Å / Num. all: 91060 / Num. obs: 89965 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8985 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q8I Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.734 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.35 Å2 / Biso mean: 39.287 Å2 / Biso min: 12.89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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