3VSY | pdb_00003vsy

High-resolution crystal structure of wild-type KSI in the apo form at neutral pH

• PDB DOI: https://doi.org/10.2210/pdb3VSY/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-16 Released: 2013-02-27 
• Deposition Author(s): Caaveiro, J.M.M., Kobe, A., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.202 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Incorporation of rapid thermodynamic data in fragment-based drug discovery.

Kobe, A., Caaveiro, J.M.M., Tashiro, S., Kajihara, D., Kikkawa, M., Mitani, T., Tsumoto, K.

(2013) J Med Chem 56: 2155-2159

• PubMed: 23419007 
• DOI: https://doi.org/10.1021/jm301603n
• Primary Citation Related Structures: 
  3VSY


• PubMed Abstract: 
  

  Fragment-based drug discovery (FBDD) has enjoyed increasing popularity in recent years. We introduce SITE (single-injection thermal extinction), a novel thermodynamic methodology that selects high-quality hits early in FBDD. SITE is a fast calorimetric competitive assay suitable for automation that captures the essence of isothermal titration calorimetry but using significantly fewer resources. We describe the principles of SITE and identify a novel family of fragment inhibitors of the enzyme ketosteroid isomerase displaying high values of enthalpic efficiency.

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Organizational Affiliation: 
• Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.

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: 29.2 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 248 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A, B	132	Pseudomonas putida	Mutation(s): 0  Gene Names: ksi 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
SO4	C [auth B], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.202 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.563	α = 90
b = 73.353	β = 90
c = 95.549	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Caaveiro, J.M.M., Kobe, A., Tsumoto, K.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description