6UAD | pdb_00006uad

Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38

• PDB DOI: https://doi.org/10.2210/pdb6UAD/pdb

• Classification: ISOMERASE
• Organism(s): Comamonas testosteroni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-10 Released: 2020-09-16 
• Deposition Author(s): Kundert, K., Thompson, M.C., Liu, L., Fraser, J.S., Kortemme, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38

Kundert, K., Thompson, M.C., Liu, L., Fraser, J.S., Kortemme, T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.41 kDa 
• Atom Count: 1,244 
• Modeled Residue Count: 121 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketosteroid isomerase with truncated and designed loop	A	124	Comamonas testosteroni	Mutation(s): 0  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
DXC	B [auth A], C [auth A]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C24 H40 O4 KXGVEGMKQFWNSR-LLQZFEROSA-N
PO4	D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.15	α = 90
b = 53.15	β = 90
c = 178.03	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Kundert, K., Thompson, M.C., Liu, L., Fraser, J.S., Kortemme, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM110089
National Science Foundation (NSF, United States)	United States	DBI-1564692

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references