4UQG | pdb_00004uqg

A new bio-isosteric base pair based on reversible bonding

PDB DOI: https://doi.org/10.2210/pdb4UQG/pdb
NAKB: 4UQG

Classification: TRANSFERASE/DNA
Organism(s): Geobacillus stearothermophilus, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-06-23 Released: 2014-12-03
Deposition Author(s): Tomas-Gamasa, M., Serdjukov, S., Su, M., Mueller, M., Carell, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.211 (Depositor), 0.219 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

"Post-it" type connected DNA created with a reversible covalent cross-link.

Tomas-Gamasa, M., Serdjukow, S., Su, M., Muller, M., Carell, T.

(2015) Angew Chem Int Ed Engl 54: 796-800

PubMed: 25446281 Search on PubMed
DOI: https://doi.org/10.1002/anie.201407854
Primary Citation Related Structures:
4UQG

PubMed Abstract:
We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible. The new principle can be used to stabilize DNA duplexes and nanostructures that otherwise require high salt concentrations, which may hinder biological applications.

Organizational Affiliation

Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München (Germany) http://www.carellgroup.de.

Macromolecule Content

Total Structure Weight: 73.02 kDa
Atom Count: 5,208
Modeled Residue Count: 599
Deposited Residue Count: 599
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	A	579	Geobacillus stearothermophilus	Mutation(s): 0 EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5 Go to UniProtKB: E1C9K5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1C9K5
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(GPAPCPC T0TPTPCPCPCP*TP)-3'	B	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
5'-D(APGPGPGPA SAYPGPGPTP*CP)-3'	C	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D	2		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] 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 A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	D	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211 (Depositor), 0.219 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.442	α = 90
b = 93.996	β = 90
c = 105.416	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2014-12-10
Changes: Database references, Other, Refinement description
Version 1.2: 2015-01-28
Changes: Database references
Version 1.3: 2017-08-23
Changes: Advisory, Data collection
Version 1.4: 2019-02-20
Changes: Data collection, Database references, Derived calculations, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary