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Category
- Diffraction » Single Crystal XRD: Protein
Booking Details
Facility Management Team and Location
Prof. Abhijit Majumder
Prof. R Murugavel
Prof. Subhabrata Dhar
Prof. I Samajdar
Facility Features, Working Principle and Specifications
X-Ray diffraction Automated crystallization set up facility Automate crystal visualization camera.
- X-Ray diffraction
- Automated crystallization set up facility
- Automate crystal visualization camera
Working Princple
In the present world of science, X-ray crystallography is the most widely used technique for determination of structures of biological macromolecules. This technique allows us to determine macromolecule structures that provides a detailed understanding of the interactions occurring at the molecular levels. Structure based drug design, study of protein-ligand interactions and structure-function relationships are the major fields where X-ray crystallography acts as a major tool. X-Ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals as they have a wavelength (in Å ~10-10 m) corresponding to the size of an atom
Principle of X-ray diffraction
Each crystal has its unit cell parameters (a,b,c and α, β, γ) and in a crystal lattice infinite sets of plane can be drawn from the lattice points. These planes can be considered as source of diffraction and designated by set of miller indices. According to Braggs laws, when a wavelength (λ nm) with an angle θ passes through a crystal (which has a set of equivalent planes with hkl) a diffracted beam with the same angle is produced from which we can calculate the d spacing of the planes.
Bragg's law
nλ = 2dsinθ
Where n : Order of diffracted beam
d : Spacing between two adjacent planes of atoms
λ : Wavelength of incident X-ray
θ : Angle of incidence of X-ray
The sets of d and intensities from protein crystals come in a unique diffraction pattern.
Diffractometer :
- Maximum rated output : 1.2 kW
- Rated tube voltage-current : 40kV; 30mA
- Target : Cu
- Radiation enclosure : Full safety shielding with plastic shield
- Scanning mode : 0 - 180o ω scan: 0-180 θ scan
- Optics : Multilayer confocal type
- Detector : Rigaku R Axis IV ++
- Beam size at the sample : 100 µm
Instructions for Registration, Sample Preparation, User Instructions and Precautionary Measures
Only online registration through the IRCC webpage will be accepted. The users will be informed about their date and time of slot by email. If the appointment is given but the user cannot come, a mail should be immediately sent to protxrd@iitb.ac.in to cancel his/her slot.
- Well isolated protein crystals obtained via sitting/hanging drop method.
- Crystals flash frozen in liquid nitrogen using appropriate cryo-protectant and maintained in a Dewar can also be provided.
- The user has to come with prepared Cryo-protectant solutions.
- Coverslips, bridges for soaking and loops appropriate for your proteins will be provided only on request.
- At the time of X-ray diffraction of crystal, the user should be present.
- Images of diffraction will be given in CD format. Please bring your own CD. USB drives are strictly not allowed due to virus threat.
- Samples and Measurement data should be collected as soon as the diffraction gets completed with a maximum duration of one week.
Charges for Analytical Services in Different Categories
Applications
- Crystal structure determination of proteins and their complexes by molecular replacement method
- Crystal structure determination of proteins by heavy atom isomorphous replacement
Sample Details
SOP, Lab Policies and Other Details
Publications
- Singh, J.; Sahil, M.; Ray, S.; Dcosta, C.; Panjikar, S.; Krishnamoorthy, G.; Mondal, J.; Anand, R. Phenol Sensing in Nature Is Modulated via a Conformational Switch Governed by Dynamic Allostery. Journal of Biological Chemistry 2022, 298 (10), 102399. https://doi.org/10.1016/j.jbc.2022.102399.
- Sharma, N.; Singh, S.; Tanwar, A. S.; Mondal, J.; Anand, R. Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. ACS Catalysis 2022, 12 (3), 1930–1944. https://doi.org/10.1021/acscatal.1c05521.
- Kesari, P.; Deshmukh, A.; Pahelkar, N.; Suryawanshi, A. B.; Rathore, I.; Mishra, V.; Dupuis, J. H.; Xiao, H.; Gustchina, A.; Abendroth, J.; Labaied, M.; Yada, R. Y.; Wlodawer, A.; Edwards, T. E.; Lorimer, D. D.; Bhaumik, P. Structures of Plasmepsin X from Plasmodium Falciparum Reveal a Novel Inactivation Mechanism of the Zymogen and Molecular Basis for Binding of Inhibitors in Mature Enzyme. Protein Science 2022, 31 (4), 882–899. https://doi.org/10.1002/pro.4279.
- Sakunthala, A.; Datta, D.; Navalkar, A.; Gadhe, L.; Kadu, P.; Patel, K.; Mehra, S.; Kumar, R.; Chatterjee, D.; Devi, J.; Sengupta, K.; Padinhateeri, R.; Maji, S. K. Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification. The Journal of Physical Chemistry Letters 2022, 13 (28), 6427–6438. https://doi.org/10.1021/acs.jpclett.2c01650.
- Kadu, P.; Gadhe, L.; Navalkar, A.; Patel, K.; Kumar, R.; Sastry, M.; Maji, S. K. Charge and Hydrophobicity of Amyloidogenic Protein/Peptide Templates Regulate the Growth and Morphology of Gold Nanoparticles. Nanoscale 2022, 14 (40), 15021–15033. https://doi.org/10.1039/d2nr01942f.
- Mehra, S.; Ahlawat, S.; Kumar, H.; Datta, D.; Navalkar, A.; Singh, N.; Patel, K.; Gadhe, L.; Kadu, P.; Kumar, R.; Jha, N. N.; Sakunthala, A.; Sawner, A. S.; Padinhateeri, R.; Udgaonkar, J. B.; Agarwal, V.; Maji, S. K. α-Synuclein Aggregation Intermediates Form Fibril Polymorphs with Distinct Prion-like Properties. Journal of Molecular Biology 2022, 434 (19), 167761. https://doi.org/10.1016/j.jmb.2022.167761.
- Chatterjee, D.; Jacob, R. S.; Ray, S.; Navalkar, A.; Singh, N.; Sengupta, S.; Gadhe, L.; Kadu, P.; Datta, D.; Paul, A.; Arunima, S.; Mehra, S.; Pindi, C.; Kumar, S.; Singru, P.; Senapati, S.; Maji, S. K. Co-Aggregation and Secondary Nucleation in the Life Cycle of Human Prolactin/Galanin Functional Amyloids. eLife 2022, 11. https://doi.org/10.7554/elife.73835.