6FJJ | pdb_00006fjj

Joint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (saccharin).

• PDB DOI: https://doi.org/10.2210/pdb6FJJ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-22 Released: 2019-02-06 
• Deposition Author(s): Fisher, S.Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.166 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

---

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative.

Koruza, K., Mahon, B.P., Blakeley, M.P., Ostermann, A., Schrader, T.E., McKenna, R., Knecht, W., Fisher, S.Z.

(2019) J Struct Biol 205: 147-154

• PubMed: 30639924 
• DOI: https://doi.org/10.1016/j.jsb.2018.12.009
• Primary Citation Related Structures: 
  6FJI, 6FJJ, 6GCY


• PubMed Abstract: 
  

  Up-regulation of carbonic anhydrase IX (CA IX) expression is an indicator of metastasis and associated with poor cancer patient prognosis. CA IX has emerged as a cancer drug target but development of isoform-specific inhibitors is challenging due to other highly conserved CA isoforms. In this study, a CA IX _mimic construct was used (CA II with seven point mutations introduced, to mimic CA IX active site) while maintaining CA II solubility that make it amenable to crystallography. The structures of CA IX _mimic unbound and in complex with saccharin (SAC) and a saccharin-glucose conjugate (SGC) were determined using joint X-ray and neutron protein crystallography. Previously, SAC and SGC have been shown to display CA isoform inhibitor selectivity in assays and X-ray crystal structures failed to reveal the basis of this selectivity. Joint X-ray and neutron crystallographic studies have shown active site residues, solvent, and H-bonding re-organization upon SAC and SGC binding. These observations highlighted the importance of residues 67 (Asn in CA II, Gln in CA IX) and 130 (Asp in CA II, Arg in CA IX) in selective CA inhibitor targeting.

---

Organizational Affiliation: 
• Lund Protein Production Platform (LP3) & Department of Biology, Lund University, 223 62 Lund, Sweden.
Department of Molecular Biology, Princeton University, 08544 Princeton, NJ, United States; Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 32610 Gainesville, United States.
Large-Scale Structures Group, Institut Laue-Langevin, 38042 Grenoble, France.
Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, 85748 Garching, Germany.
Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), 85747 Garching, Germany.
Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 32610 Gainesville, United States.
Lund Protein Production Platform (LP3) & Department of Biology, Lund University, 223 62 Lund, Sweden; Scientific Activities Division, European Spallation Source ERIC (ESS), 221 00 Lund, Sweden. Electronic address: [e-mail].

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: 29.45 kDa 
• Atom Count: 2,287 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 7  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LSA	C [auth A]	1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE C7 H5 N O3 S CVHZOJJKTDOEJC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.166 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.53	α = 90
b = 41.83	β = 104.04
c = 72.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Fisher, S.Z.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description