Download MendeleyDirected evolution of a highly efficient TNA polymerase achieved by homologous recombination
Maola, V.A., Yik, E.J., Hajjar, M., Lee, J.J., Holguin, M.J., Quijano, R.N., Nguyen, K.K., Ho, K.L., Medina, J.V., Chim, N., Chaput, J.C.(2024) Nat Catal
8T3X
TNA polymerase, closed ternary
- PDB DOI: https://doi.org/10.2210/pdb8T3X/pdb
- NAKB: 8T3X
- Classification: TRANSFERASE/DNA
- Organism(s): Thermococcus kodakarensis, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2023-06-07 Released: 2024-08-28
- Funding Organization(s): National Science Foundation (NSF, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.73 ?
- R-Value Free: 0.301 (Depositor), 0.300 (DCC)
- R-Value Work: 0.242 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.247 (Depositor)
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 |
| 10-92, TNA polymerase | 760 | Thermococcus kodakarensis | Mutation(s): 51 EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore D0VWU9 Go to UniProtKB: D0VWU9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VWU9 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Template | B [auth T] | 15 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Primer | C [auth P] | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 9O7 Query on 9O7 | D [auth A] | [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate C9 H14 N5 O12 P3 AWDFERYZHFHVNT-AFEQZKEHSA-N |  | ||
| EPE Query on EPE | F [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.73 ?
- R-Value Free: 0.301 (Depositor), 0.300 (DCC)
- R-Value Work: 0.242 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.247 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 76.869 | ¦Á = 90 |
| b = 99.525 | ¦Â = 90 |
| c = 110.727 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-08-28 Deposition Author(s): Maola, V., Chaput, J., Chim, N.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (NSF, United States) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-08-28
Type: Initial release - Version 1.1: 2024-10-30
Changes: Database references, Structure summary
