4BWJ | pdb_00004bwj

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 (Depositor), 0.211 (DCC)
R-Value Work:
0.158 (Depositor)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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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 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
Modeled Residue Count: 565
Deposited Residue Count: 568
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19821
Sequence Annotations Expand
Reference Sequence

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

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Molecule	Chains	Length	Organism
Entity ID: 3
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 I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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 (Depositor), 0.211 (DCC)
R-Value Work: 0.158 (Depositor)
R-Value Observed: 0.161 (Depositor)

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

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Ligand Structure Quality Assessment

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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