6RQW

X-ray crystal structure of perdeuterated (D) small monoclinic unit cell CA IX SV.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.488 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX.

Koruza, K.Lafumat, B.Nyblom, M.Mahon, B.P.Knecht, W.McKenna, R.Fisher, S.Z.

(2019) Acta Crystallogr D Struct Biol 75: 895-903

  • DOI: 10.1107/S2059798319010027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural stud ...

    Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX-inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IX SV ; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IX SV for crystallographic studies and their structural comparison are described. Four CA IX SV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal contacts and packing reveals different arrangements of CA IX SV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IX SV for neutron protein crystallography.


    Organizational Affiliation

    Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.,Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 9
A
256Homo sapiensMutation(s): 6 
Gene Names: CA9 (G250, MN)
EC: 4.2.1.1
Find proteins for Q16790 (Homo sapiens)
Go to Gene View: CA9
Go to UniProtKB:  Q16790
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.488 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.390α = 90.00
b = 65.090β = 114.71
c = 46.600γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-16 
  • Released Date: 2019-09-11 
  • Deposition Author(s): Fisher, Z., Koruza, K.

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references