5OL5 | pdb_00005ol5

Crystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein

• PDB DOI: https://doi.org/10.2210/pdb5OL5/pdb

• Classification: SPLICING
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-26 Released: 2017-09-27 
• Deposition Author(s): Kick, L.M., Schneider, S.
• Funding Organization(s): Center for Integrated Protein Science, German Research Foundation, Fonds der chemischen Industrie

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation.

Kick, L.M., Harteis, S., Koch, M.F., Schneider, S.

(2017) Chembiochem 18: 2242-2246

• PubMed: 28914478 
• DOI: https://doi.org/10.1002/cbic.201700503
• Primary Citation Related Structures: 
  5OL1, 5OL5, 5OL6, 5OL7


• PubMed Abstract: 
  

  Inteins carry out protein-splicing reactions, which are used in protein chemistry, protein engineering and biotechnological applications. Rearrangement of the order of the domains in split-inteins results in head-to-tail cyclisation of the target sequence, which can be used for genetic encoding and expression of libraries of cyclic peptides (CPs). The efficiency of the splicing reaction depends on the target sequence. Here we used mass spectrometry to assess in vivo cyclic peptide formation from different hexameric target sequences by the DnaE split-inteins from Synechocystis sp. and Nostoc punctiforme, revealing a strong impact of the target sequence and of the intein on the intracellular peptide concentration. Furthermore, we determined the crystal structures of their pre-splicing complexes, which allowed us to identify F-block Asp17 as crucial for the DnaE-mediated splicing reaction.

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Organizational Affiliation: 
• Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.98 kDa 
• Atom Count: 4,607 
• Modeled Residue Count: 560 
• Deposited Residue Count: 684 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit alpha,DNA polymerase III subunit alpha	A, B	171	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: dnaE-N, slr0603, dnaE-C, sll1572 EC: 2.7.7.7
UniProt
Find proteins for P74750 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74750  Go to UniProtKB:  P74750

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit alpha,DNA polymerase III subunit alpha	C, D	171	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: dnaE-N, slr0603, dnaE-C, sll1572 EC: 2.7.7.7
UniProt
Find proteins for P74750 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74750  Go to UniProtKB:  P74750

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	G [auth C], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO	E [auth A], I [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.12	α = 90
b = 92.129	β = 90
c = 110.448	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Kick, L.M., Schneider, S.

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Funding Organization	Location	Grant Number
Center for Integrated Protein Science	Germany	--
German Research Foundation	Germany	SCHN1273
German Research Foundation	Germany	SFB749
Fonds der chemischen Industrie	Germany	--

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-07-10
  Changes: Data collection
• Version 1.4: 2019-11-20
  Changes: Derived calculations
• Version 1.5: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description