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 
• Deposition Author(s): Holzberger, B., Obeid, S., Welte, W., Diederichs, K., Marx, A.

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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 

Starting Model: experimental

Literature

Structural 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

• DOI: https://doi.org/10.1039/C2SC20545A

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.87 kDa 
• Atom Count: 5,133 
• Modelled Residue Count: 567 
• Deposited Residue Count: 568 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA primer	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA template	C	16	N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCT	F [auth A]	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C9 H16 N3 O12 P3 ARLKCWCREKRROD-POYBYMJQSA-N
GOL	E [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	G [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Holzberger, B., Obeid, S., Welte, W., Diederichs, K., Marx, A.

Revision History  

• 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