3NHX | pdb_00003nhx

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound

• PDB DOI: https://doi.org/10.2210/pdb3NHX/pdb

• Classification: ISOMERASE
• Organism(s): Comamonas testosteroni
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-06-14 Released: 2011-11-23 
• Deposition Author(s): Gonzalez, A., Tsai, Y., Schwans, J., Ruben, E., Sunden, F., Herschlag, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound

Schwans, J., Ruben, E., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D.

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)

Macromolecule Content 

• Total Structure Weight: 14.66 kDa 
• Atom Count: 1,280 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A	125	Comamonas testosteroni	Mutation(s): 1  Gene Names: ksi EC: 5.3.3.1
UniProt
Find proteins for P00947 (Comamonas testosteroni) Explore P00947  Go to UniProtKB:  P00947

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASD	B [auth A]	4-ANDROSTENE-3-17-DIONE C19 H26 O2 AEMFNILZOJDQLW-QAGGRKNESA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.28	α = 90
b = 61.28	β = 90
c = 142.861	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-23 
Deposition Author(s): Gonzalez, A., Tsai, Y., Schwans, J., Ruben, E., Sunden, F., Herschlag, D.

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description