Download MendeleyStructures of a High-fidelity DNA Polymerase
Wang, W., Hellinga, H.W., Beese, L.S.To be published.
4F3O
DNA Polymerase I Large Fragment Complex 5
- PDB DOI: https://doi.org/10.2210/pdb4F3O/pdb
- NAKB: 4F3O
- Classification: Transferase/DNA
- Organism(s): Geobacillus kaustophilus HTA426, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2012-05-09 Released: 2013-07-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.57 Å
- R-Value Free: 0.204
- R-Value Work: 0.179
- R-Value Observed: 0.180
Starting Model: experimental
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This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase | A, B [auth D] | 592 | Geobacillus kaustophilus HTA426 | Mutation(s): 2 Gene Names: GK2730, polA EC: 2.7.7.7 |  |
UniProt | |||||
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KWC1 Go to UniProtKB: Q5KWC1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5KWC1 | ||||
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*CP*TP*GP*AP*CP*TP*CP*(2DT))-3') | C [auth B], E | 9 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') | D [auth C], F | 13 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D3T Query on D3T | K [auth D] | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O13 P3 URGJWIFLBWJRMF-JGVFFNPUSA-N |  | ||
| MPD Query on MPD | I [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| SO4 Query on SO4 | G [auth A], H [auth A], L [auth D], M [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| MN Query on MN | J [auth A], N [auth D] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.57 Å
- R-Value Free: 0.204
- R-Value Work: 0.179
- R-Value Observed: 0.180
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.83 | α = 90 |
| b = 109.33 | β = 90 |
| c = 150.11 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2013-07-24 Deposition Author(s): Wang, W., Beese, L.S.
Revision History (Full details and data files)
- Version 1.0: 2013-07-24
Type: Initial release - Version 1.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
