Download MendeleyStructural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein
Holzberger, B., Obeid, S., Welte, W., Diederichs, K., Marx, A.(2012) Chem Sci 3: 2924-2931
4DLE
Ternary Structure of the large Fragment of Taq DNA Polymerase: 4-Fluoroproline Variant
- PDB DOI: https://doi.org/10.2210/pdb4DLE/pdb
- NAKB: 4DLE
- Classification: Transferase/DNA
- Organism(s): Thermus aquaticus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-02-06 Released: 2012-11-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.44 Å
- R-Value Free: 0.282
- R-Value Work: 0.233
- R-Value Observed: 0.235
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase I, thermostable | 540 | Thermus aquaticus | Mutation(s): 0 Gene Names: polA, pol1 EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for P19821 (Thermus aquaticus) Explore P19821 Go to UniProtKB: P19821 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P19821 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA primer | 12 | N/A |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DCT Query on DCT | F [auth A] | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C9 H16 N3 O12 P3 ARLKCWCREKRROD-POYBYMJQSA-N |  | ||
| GOL Query on GOL | E [auth A], I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MN Query on MN | G [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| FP9 Query on FP9 | A | L-PEPTIDE LINKING | C5 H8 F N O2 |  | PRO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.44 Å
- R-Value Free: 0.282
- R-Value Work: 0.233
- R-Value Observed: 0.235
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 109.619 | α = 90 |
| b = 109.619 | β = 90 |
| c = 91.011 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XDS | data scaling |
| PHENIX | model building |
| PHENIX | refinement |
| XDS | data reduction |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2012-11-28 Deposition Author(s): Holzberger, B., Obeid, S., Welte, W., Diederichs, K., Marx, A.
Revision History (Full details and data files)
- Version 1.0: 2012-11-28
Type: Initial release - Version 1.1: 2014-01-15
Changes: Derived calculations - Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-12-06
Changes: Data collection
