7DVK

PyrI4 in complex with intermolecular Diels-Alder product

• PDB DOI: https://doi.org/10.2210/pdb7DVK/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces rugosporus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2021-01-13 Released: 2021-08-18 
• Deposition Author(s): Kashyap, R., Addlagatta, A.
• Funding Organization(s): Council of Scientific & Industrial Research (CSIR), Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates.

Kashyap, R., Yerra, N.V., Oja, J., Bala, S., Potuganti, R., Thota, J.R., Alla, M., Pal, D., Addlagatta, A.

(2021) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-021-00552-9

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 83.91 kDa 
• Atom Count: 5,054 
• Modelled Residue Count: 652 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spiro-conjugate synthase	A, B, C, D	194	Streptomyces rugosporus	Mutation(s): 0  Gene Names: pyrI4 EC: 5.5.1
UniProt
Find proteins for K7QVW7 (Streptomyces rugosporus) Explore K7QVW7  Go to UniProtKB:  K7QVW7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HOF (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	methyl 4-[[(1S,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamoyloxymethyl]benzoate C19 H24 N2 O5 VSPPPQJKRCRPEW-HOTGVXAUSA-N
GOL	F [auth A], H [auth B], J [auth C], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.959	α = 90
b = 102.959	β = 90
c = 168.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Kashyap, R., Addlagatta, A.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	33/2018/MD-FTT&FTC-ANB
Science and Engineering Research Board (SERB)	India	EMR/2015/000461
Science and Engineering Research Board (SERB)	India	CRG/2019/006013

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description