4BWJ

KlenTaq mutant in complex with DNA and ddCTP

PDB DOI: https://doi.org/10.2210/pdb4BWJ/pdb
NAKB: 4BWJ

Classification: TRANSFERASE/DNA
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.201
R-Value Work: 0.158
R-Value Observed: 0.161

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/anie.201306655
Primary Citation of Related Structures:
4BWJ, 4BWM

Organizational Affiliation

Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany).

Macromolecule Content

Total Structure Weight: 70.21 kDa
Atom Count: 5,394
Modelled Residue Count: 565
Deposited Residue Count: 568
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19821
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(GPAPCPCPAPCPGPGPCPGPCPDOCP)-3'	B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(APGPGPGPCPGPCPCPGPTPGPGPTPCP)-3'	C	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCT Query on DCT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₂ P₃ ARLKCWCREKRROD-POYBYMJQSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.201
R-Value Work: 0.158
R-Value Observed: 0.161
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.143	α = 90
b = 108.143	β = 90
c = 89.81	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2013-10-02
Changes: Atomic model
Version 1.2: 2013-10-23
Changes: Database references
Version 1.3: 2013-12-25
Changes: Database references
Version 1.4: 2015-09-23
Changes: Data collection, Database references, Source and taxonomy
Version 1.5: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.6: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description