Download MendeleyStructural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase
Walsh, A.R., Beese, L.S., Wu, E.Y.To be published.
6UEU
Crystal structure of BF DNA polymerase F710Y mutant bound to tetrahydrofuran and dATP
- PDB DOI: https://doi.org/10.2210/pdb6UEU/pdb
- NAKB: 6UEU
- Classification: REPLICATION
- Organism(s): Geobacillus stearothermophilus, synthetic construct
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): Yes
- Deposited: 2019-09-23 Released: 2020-09-30
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242
- R-Value Work: 0.200
- R-Value Observed: 0.202
Starting Model: experimental
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This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase I | A, B [auth D] | 580 | Geobacillus stearothermophilus | Mutation(s): 1 Gene Names: DPO1, polA EC: 2.7.7.7 |  |
UniProt | |||||
Find proteins for D9N168 (Geobacillus stearothermophilus) Explore D9N168 Go to UniProtKB: D9N168 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D9N168 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3') | C [auth B], E | 9 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3') | D [auth C], F | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DTP Query on DTP | I [auth A], J [auth D] | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N |  | ||
| MPD Query on MPD | L [auth D] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| SO4 Query on SO4 | K [auth D] | 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 | G, H | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242
- R-Value Work: 0.200
- R-Value Observed: 0.202
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.875 | α = 90 |
| b = 109.068 | β = 90 |
| c = 150.096 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-09-30 Deposition Author(s): Wu, E.Y., Beese, L.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | RO1 GM091487 |
Revision History (Full details and data files)
- Version 1.0: 2020-09-30
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
