4CDL | pdb_00004cdl

Crystal Structure of Retro-aldolase RA110.4-6 Complexed with Inhibitor 1-(6-methoxy-2-naphthalenyl)-1,3-butanedione

• PDB DOI: https://doi.org/10.2210/pdb4CDL/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-11-01 Released: 2014-11-12 
• Deposition Author(s): Pinkas, D.M., Studer, S., Obexer, R., Giger, L., Gruetter, M.G., Baker, D., Hilvert, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.297 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Active Site Plasticity of a Computationally Designed Retro-Aldolase Enzyme

Studer, S., Obexer, R., Giger, L., Pinkas, D.M., Gruetter, M.G., Baker, D., Hilvert, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.38 kDa 
• Atom Count: 1,067 
• Modeled Residue Count: 126 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROID DELTA-ISOMERASE	A	141	Pseudomonas putida	Mutation(s): 18  EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445  Go to UniProtKB:  P07445

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLK	B [auth A]	(2E)-1-(6-methoxynaphthalen-2-yl)but-2-en-1-one C15 H14 O2 MDAHFYAQSIDRGG-ONEGZZNKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.297 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.58	α = 90
b = 51.58	β = 90
c = 198.64	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Pinkas, D.M., Studer, S., Obexer, R., Giger, L., Gruetter, M.G., Baker, D., Hilvert, D.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Derived calculations, Other
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary