Download MendeleyInsights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant
Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H., Wang, J.To be published.
3CFR
Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 2
- PDB DOI: https://doi.org/10.2210/pdb3CFR/pdb
- NAKB: 3CFR
- Classification: Transferase/DNA
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2008-03-04 Released: 2009-03-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.266
- R-Value Work: 0.192
- R-Value Observed: 0.196
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase | C [auth A] | 909 | N/A | Mutation(s): 3 Gene Names: 43 EC: 2.7.7.7 |  |
UniProt | |||||
Find proteins for Q38087 (Escherichia phage RB69) Explore Q38087 Go to UniProtKB: Q38087 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q38087 | ||||
Protein Feature ViewExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*DTP*DCP*DAP*DAP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3') | A [auth T] | 18 | N/A |  | |
Protein Feature ViewExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*(DOC))-3') | B [auth P] | 13 | N/A |  | |
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TTP Query on TTP | J [auth A] | THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N |  | Ligand Interaction | |
| CA Query on CA | D [auth A], E [auth A], F [auth A], G [auth A], H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | I [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.266
- R-Value Work: 0.192
- R-Value Observed: 0.196
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.958 | α = 90 |
| b = 119.769 | β = 90 |
| c = 130.43 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2009-03-10 Deposition Author(s): Wang, J., Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H.
Revision History (Full details and data files)
- Version 1.0: 2009-03-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-10-20
Changes: Database references, Derived calculations - Version 1.3: 2023-08-30
Changes: Data collection, Refinement description
