7PXO

Structure of the Diels Alderase enzyme AbyU, from Micromonospora maris, co-crystallised with a non transformable substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb7PXO/pdb

• Classification: LIGASE
• Organism(s): Micromonospora maris AB-18-032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-08 Released: 2022-11-16 
• Deposition Author(s): Back, C.R., Race, P.R.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.245 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Delineation of the Complete Reaction Cycle of a Natural Diels-Alderase

Maschio, L., Mbatha, S.Z., Johns, S.T., Back, C.R., Zorn, K., Stach, J.E.M., Hayes, M.A., van der Kamp, M.W., Willis, C.L., Pudney, C.R., Burston, S.G., Race, P.R.

To be published.

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 Evidence: gel filtration

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: 72.83 kDa 
• Atom Count: 4,334 
• Modelled Residue Count: 537 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YD repeat-containing protein	A [auth D], B [auth A], C [auth B], D [auth C]	160	Micromonospora maris AB-18-032	Mutation(s): 0  Gene Names: VAB18032_16470
UniProt
Find proteins for F4F7G1 (Micromonospora maris (strain DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032)) Explore F4F7G1  Go to UniProtKB:  F4F7G1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8IF (Subject of Investigation/LOI)	E [auth D], G [auth A], H [auth B]	(2~{S},4~{S})-1-(4-methoxy-5-methyl-2-oxidanylidene-3~{H}-furan-3-yl)-2,4-dimethyl-dodecane-1,5-dione C20 H32 O5 ULKZMMBTEMBHMN-GRDNDAEWSA-N
EPE	F [auth D], I [auth C], J [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.245 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.57	α = 90
b = 61.56	β = 112.96
c = 87.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Back, C.R., Race, P.R.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T001968/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M012107/1
Engineering and Physical Sciences Research Council	United Kingdom	BB/L01386X/1
Engineering and Physical Sciences Research Council	United Kingdom	EP/L016494/1

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 2.0: 2024-04-24
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary