4BWM | pdb_00004bwm

KlenTaq mutant in complex with a RNA/DNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb4BWM/pdb
• NAKB: 4BWM

• Classification: TRANSFERASE/DNA/RNA
• Organism(s): Thermus aquaticus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-07-03 Released: 2013-09-18 
• Deposition Author(s): Blatter, N., Bergen, K., Welte, W., Diederichs, K., Marx, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of an RNA-Reading Thermostable DNA Polymerase.

Blatter, N., Bergen, K., Nolte, O., Welte, W., Diederichs, K., Mayer, J., Wieland, M., Marx, A.

(2013) Angew Chem Int Ed Engl 52: 11935

• PubMed: 24106012 
• DOI: https://doi.org/10.1002/anie.201306655
• Primary Citation Related Structures: 
  4BWJ, 4BWM

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Organizational Affiliation: 
• Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of 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: 70.65 kDa 
• Atom Count: 5,522 
• Modeled Residue Count: 562 
• 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): 4  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
5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3'	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3'	C [auth G]	16	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCT	D [auth A]	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C9 H16 N3 O12 P3 ARLKCWCREKRROD-POYBYMJQSA-N
FMT	H [auth A], I [auth A], J [auth A], M [auth G]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.192	α = 90
b = 86.282	β = 90
c = 63.094	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Blatter, N., Bergen, K., Welte, W., Diederichs, K., Marx, A.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2015-09-23
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description