Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.10 kDa 
• Atom Count: 4961 
• Modelled Residue Count: 601 
• Deposited Residue Count: 601 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2XY7

Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus

• PDB DOI: 10.2210/pdb2XY7/pdb
• NDB: NA1230

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


• Deposited: 2010-11-15 Released: 2011-07-27 
• Deposition Author(s): Kaul, C., Mueller, M., Wagner, M., Schneider, S., Carell, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.284 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Literature

Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair.

Kaul, C., Mueller, M., Wagner, M., Schneider, S., Carell, T.

(2011) Nat Chem 3: 794

• PubMed: 21941252 
• DOI: 10.1038/nchem.1117
• Primary Citation of Related Structures:  
  2XY5, 2XY6, 2XY7


• PubMed Abstract: 
  

The universal genetic code relies on two hydrogen-bonded Watson-Crick base pairs that can form 64 triplet codons. This places a limit on the number of amino acids that can be encoded, which has motivated efforts to create synthetic base pairs that are orthogonal to the natural ones. An additional base pair would result in another 61 triplet codons. Artificial organic base pairs have been described in enzymatic incorporation studies, and inorganic T-Hg-T and C-Ag-C base pairs have been reported to form in primer extension studies. Here, we demonstrate a metal base pair that is fully orthogonal and can be replicated, and can even be amplified by polymerase chain reaction in the presence of the canonical pairs dA:dT and dG:dC. Crystal structures of a dS-Cu-dS base pair inside a polymerase show that reversible chemistry is possible directly inside the polymerase, which enables the efficient copying of the inorganic crosslink. The results open up the possibility of replicating and amplifying artificial inorganic DNA nanostructures by extending the genetic alphabet.

---

Organizational Affiliation: 

Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstrasse 5-13, D-81377 Munich, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE I	A	580	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: polA EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5  Go to UniProtKB:  E1C9K5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3'	B	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3'	C	11	synthetic construct

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	D	sucrose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.284 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.037	α = 90
b = 94.022	β = 90
c = 106.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-15 
• Released Date: 2011-07-27 
Deposition Author(s): Kaul, C., Mueller, M., Wagner, M., Schneider, S., Carell, T.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-10-05
  Changes: Database references
• Version 1.2: 2012-03-28
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary