3TAN
Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-1) Position
- PDB DOI: https://doi.org/10.2210/pdb3TAN/pdb
- NAKB: 3TAN
- Classification: TRANSFERASE/DNA
- Organism(s): Geobacillus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2011-08-04 Released: 2011-10-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.184
- R-Value Work: 0.170
- R-Value Observed: 0.170
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase I | 592 | Geobacillus | Mutation(s): 0 EC: 2.7.7.7 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*C)-3' | 10 | N/A |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DCP Query on DCP | I [auth A] | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N |  | ||
| SO4 Query on SO4 | E [auth A], F [auth A], G [auth A], H [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | D | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.184
- R-Value Work: 0.170
- R-Value Observed: 0.170
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.43 | α = 90 |
| b = 93.01 | β = 90 |
| c = 105.33 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2011-10-19 Deposition Author(s): Wang, W., Beese, L.S.
Revision History (Full details and data files)
- Version 1.0: 2011-10-19
Type: Initial release - Version 1.1: 2011-11-16
Changes: Database references - Version 1.2: 2014-04-02
Changes: Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
