2XY5 | pdb_00002xy5

Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.235 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/nchem.1117
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 73.33 kDa 
  • Atom Count: 5,227 
  • Modeled Residue Count: 601 
  • Deposited Residue Count: 601 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE I581Geobacillus stearothermophilusMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3'10synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3'10synthetic construct
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose
D
2N/A
Glycosylation Resources
GlyTouCan: G49187ZK
GlyCosmos: G49187ZK

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD

Query on MRD



Download:Ideal Coordinates CCD File
I [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU1

Query on CU1



Download:Ideal Coordinates CCD File
J [auth C]COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
EDN

Query on EDN



Download:Ideal Coordinates CCD File
K [auth C]ETHANE-1,2-DIAMINE
C2 H8 N2
PIICEJLVQHRZGT-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.235 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.171α = 90
b = 93.469β = 90
c = 105.591γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2011-10-05
    Changes: Database references, Other
  • Version 1.2: 2012-05-30
    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
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary