3M8S

Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-methylated dTTP

• PDB DOI: https://doi.org/10.2210/pdb3M8S/pdb
• NAKB: 3M8S

• Classification: Transferase/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-19 Released: 2010-07-07 
• Deposition Author(s): Diederichs, K., Marx, A., Betz, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Structures of DNA polymerases caught processing size-augmented nucleotide probes.

Betz, K., Streckenbach, F., Schnur, A., Exner, T., Welte, W., Diederichs, K., Marx, A.

(2010) Angew Chem Int Ed Engl 49: 5181-5184

• PubMed: 20572212 
• DOI: https://doi.org/10.1002/anie.200905724
• Primary Citation of Related Structures:  
  3M8R, 3M8S

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Organizational Affiliation: 

Department of Chemistry, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.

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: 72.2 kDa 
• Atom Count: 5,057 
• 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 (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	C	16	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	I [auth A]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
HXB	D [auth A]	4'-methylthymidine 5'-(tetrahydrogen triphosphate) C11 H19 N2 O14 P3 IUVOCYKHODEDJI-VAOFZXAKSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth A], M [auth B], N [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	J [auth A], K [auth A], L [auth A], O [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.742	α = 90
b = 108.742	β = 90
c = 90.755	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Diederichs, K., Marx, A., Betz, K.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description