8JOJ

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate

• PDB DOI: https://doi.org/10.2210/pdb8JOJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodococcus erythropolis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-07 Released: 2023-07-12 
• Deposition Author(s): Hu, Y.L., Li, X., Cheng, X.Y., Song, S.K., Su, Z.D.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate

Song, S.K., Hu, Y.L., Li, X., Su, Z.D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 55.85 kDa 
• Atom Count: 3,925 
• Modelled Residue Count: 523 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ketosteroid dehydrogenase	A	523	Rhodococcus erythropolis	Mutation(s): 0  Gene Names: kstD1, BS297_24040, rerp_49010, RERY_47440 EC: 1.3.99.4
UniProt
Find proteins for Q9RA02 (Rhodococcus erythropolis) Explore Q9RA02  Go to UniProtKB:  Q9RA02

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UU0 (Subject of Investigation/LOI)	C [auth A]	9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate C24 H32 O6 FOTDGVYUEIORAP-ITJRCREZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.603	α = 90
b = 119.603	β = 90
c = 117.304	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Hu, Y.L., Li, X., Cheng, X.Y., Song, S.K., Su, Z.D.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection