Protein Crystallography Facility

External users: registration to be carried out only through I-STEM portal
Additional information about sample and analysis details should be filled in the pdf form provided in the I-STEM portal under “DOWNLOAD CSRF”

Internal users (IITB): registration to be carried out only through DRONA portal
Additional information about sample and analysis details should be filled in the pdf form provided here.

Registartion Form.pdf (70.93 KB)
Make
Rigaku MicroMax-007HF
Model
R-Axis IV++
Facility Status
Working
Date of Installation
Facility Management Division
Centre for Sophisticated Instruments and Facilities (CSIF)

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Category

  • Diffraction » Single Crystal XRD: Protein

Booking Details

Slot Booking Link
Click here for Internal User Booking!
I-STEM Slot Booking link for External User
Booking available for
Internal and External Both
Available Equipment/ Mode of use
Screening/ diffraction of protein and DNA/RNA crystals for preliminary diffraction to assess and enhance quality.
Fibre diffraction of bio-fibres (amyloids).
Atomic level high resolution data collection for solving 3D structures of the bio molecules
Automated crystallisation robots for setting up soluble and membrane protein crystals

Facility Management Team and Location

Facility In Charge
Prof. Ruchi Anand
Facility Manager
Ms. Harshada Malvi
Facility Operator
Ms. Harshada Malvi
Facility Management Members
Prof. Ruchi Anand (Convener) - Chemistry, Prof. Prasenjit Bhaumik - BSBE, Prof. Ashutosh Kumar - BSBE, Prof. Subhabrata Dhar – Physics, Prof. Samir Maji – BSBE, Prof. Sandip Kaledhonkar - BSBE
Department
CRNTS
Lab Email ID
protxrd@iitb.ac.in
Facility Location
Room No. 103, Ground floor,SAIF, I.I.T. Bombay, Powai, Mumbai - 400 076.
Lab Phone No
02221596854

Facility Features, Working Principle and Specifications

Facility Description

Facility Description

Our protein crystallography facility is a dedicated laboratory designed to facilitate the research and analysis of protein structures through X-ray crystallography, a leading and widely used method for determining the 3D atomic-level structures of proteins. The facility is equipped with an X-ray diffractometer and automated crystallization robots to support efficient and high-quality experimentation.

Features Working Principle

Protein X-ray crystallography is a powerful technique used to determine the 3D atomic structure of proteins. The process involves several key steps:

  1. Crystallisation: Purified protein is crystallised into highly ordered, repeating lattices that allow for X-ray diffraction.
  2. X-ray Exposure: The protein crystal is exposed to X-rays, which are scattered by the atoms in the crystal, producing a diffraction pattern.
  3. Data Collection: A series of diffraction patterns is collected by rotating the crystal in the X-ray beam, capturing data from different angles.
  4. Phase Problem: The diffraction data provide amplitude and orientation, but not phase information. Phasing methods like molecular replacement or heavy atom derivatization are used to solve this problem.
  5. Electron Density Map: The data, with phase information, are used to calculate an electron density map, which shows the positions of atoms in the crystal.
  6. Model Building and Refinement: Researchers build an atomic model based on the electron density map and refine it by adjusting atom positions to minimise discrepancies with the data.
  7. Validation: The final model is validated for accuracy using various quality metrics and tests.
Body Specification

Diffractometer:

  • Maximum Rated Output: 1.2 kW
  • Rated Tube Voltage-Current: 40 kV; 30 mA
  • Target: Copper (Cu)
  • Radiation Enclosure: Full safety shielding with plastic cover
  • Scanning Mode: 0-180° ω scan, 0-180° θ scan
  • Optics: Multilayer confocal type
  • Detector: Rigaku R Axis IV++
  • Beam Size at the Sample: 100 µm

Mosquito Crystallization Robot:

  • Designed for screening soluble and membrane proteins (LCP).
  • Capable of performing hanging drop, sitting drop, microbatch, microseeding, and additive screening.
  • Automated syringe dispenser for accurate liquid handling.
  • Highly precise and rapid automated plate setups.
  • Dispense volume range: 25 nL to 1200 nL (protein), 70 µL (well solution).
  • Ensures zero cross-contamination with no washing steps required.

Phoenix Crystallization Robot:

  • Ideal for screening soluble proteins.
  • Supports sitting drop, hanging drop, and microbatch reactions.
  • Dispense volume range: 100 nL to 100 µL.
  • Rapid dispensing (< 50 seconds) of screen and protein, minimizing evaporation issues.
  • Flexible dispensing needles.
  • Multiple proteins can be quickly dispensed into multi-well plates.

Sample Preparation, User Instructions and Precautionary Measures

Instruction for Sample Preparation
  • Well-isolated protein crystals from crystallisation plates should be supplied for the slot.
  • Crystals can also be flash-frozen in liquid nitrogen with the appropriate cryoprotectant, stored in a Dewar, and sent to us for the slot.
  • Users must provide their own pre-prepared cryoprotectant solutions.
  • Cover-slips, soaking bridges, and loops suitable for your proteins will be provided upon request, with additional charges applicable.
  • For crystallisation, purified proteins with a sufficient concentration should be provided.
User Instructions and Precautionary Measures
  • The user must be present during the X-ray diffraction of the crystal or setting up crystallisation trays.
  • Diffraction images will be provided on a CD. Please bring your own CD, as USB drives are strictly prohibited due to virus concerns.
  • Samples and measurement data must be collected immediately after the diffraction is completed, with a maximum allowed duration of one week.

Charges for Analytical Services in Different Categories

Usage Charges

Charges for Internal Users (18% GST applicable)

Sr. No.OrganizationScreening per dayData collection per sample Crystallization tray setup using robots per tray
1Academic Institution3,500/-5,000/-3000/-
2Industries & Non – Government Agencies20,000/- 50,000/- 25,000/-

Charges for External Users (18% GST applicable)

Sr. No.OrganizationScreening per dayData collection per sample Crystallization tray setup using robots per tray
1Academic Institution4,500/-7,000/-4,000/-
2Industries & Non – Government Agencies20,000/- 50,000/- 25,000/-

Applications

  • Understanding Protein Function: It reveals how protein structures relate to their biological roles, aiding in the study of enzyme mechanisms, signal transduction, and receptor-ligand interactions.
  • Drug Design: Structural insights guide the development of targeted drugs, such as enzyme inhibitors, antibodies, and small molecule therapeutics.
  • Protein-Ligand Interactions: Crystallography helps identify binding sites for small molecules, improving drug discovery and design.
  • Studying Protein Complexes: It provides insights into how proteins interact in larger complexes, crucial for understanding cellular processes.
  • Disease Mechanisms: It aids in understanding how mutations affect protein function, helping in the development of treatments for genetic diseases.
  • Structural Genomics: It contributes to mapping the structures of proteins across various organisms, advancing biological knowledge.
  • Viral and Bacterial Pathogens: Crystallography is used to design antiviral drugs and antibiotics by studying viral and bacterial proteins.
  • Biotechnology: It supports enzyme engineering and the development of industrial enzymes and biocatalysts.

Sample Details

SOP, Lab Policies and Other Details

Publications

2022:

  1. 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. DOI
  2. 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. DOI
  3. 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. DOI
  4. 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. DOI
  5. 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. DOI
  6. 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. DOI
  7. 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. DOI

2021:

  1. Godsora, B. K. J., Prakash, P., Punekar, N. S., Bhaumik, P. "Molecular Insights into the Inhibition of Glutamate Dehydrogenase by the Dicarboxylic Acid Metabolites." Proteins: Structure, Function, and Bioinformatics, 2021, 90(3), 810–823. DOI

2020:

  1. Sharma, N., Ahalawat, N., Sandhu, P., Strauss, E., Mondal, J., Anand, R. "Role of Allosteric Switches and Adaptor Domains in Long-Distance Cross-Talk and Transient Tunnel Formation." Science Advances, 2020, 6(14). DOI
  2. Rathore, I., Mishra, V., Patel, C., Xiao, H., Gustchina, A., Wlodawer, A., Yada, R. Y., Bhaumik, P. "Activation Mechanism of Plasmepsins, Pepsin‐like Aspartic Proteases from Plasmodium, Follows a Unique Trans‐Activation Pathway." The FEBS Journal, 2020, 288(2), 678–698. DOI
  3. Badgujar, D. C., Anil, A., Green, A. E., Surve, M. V., Madhavan, S., Beckett, A., Prior, I. A., Godsora, B. K., Patil, S. B., More, P. K., Sarkar, S. G., Mitchell, A., Banerjee, R., Phale, P. S., Mitchell, T. J., Neill, D. R., Bhaumik, P., Banerjee, A. "Structural Insights into Loss of Function of a Pore Forming Toxin and Its Role in Pneumococcal Adaptation to an Intracellular Lifestyle." PLOS Pathogens, 2020, 16(11), e1009016. DOI
  4. Kadu, P., Pandey, S., Neekhra, S., Kumar, R., Gadhe, L., Srivastava, R., Sastry, M., Maji, S. K. "Machine-Free Polymerase Chain Reaction with Triangular Gold and Silver Nanoparticles." The Journal of Physical Chemistry Letters, 2020, 11(24), 10489–10496. DOI

2019:

  1. Yarramala, D. S., Prakash, P., Ranade, D. S., Doshi, S., Kulkarni, P. P., Bhaumik, P., Rao, C. P. "Cytotoxicity of Apo Bovine α-Lactalbumin Complexed with La3+ on Cancer Cells Supported by Its High Resolution Crystal Structure." Scientific Reports, 2019, 9(1), 1780. DOI

2018:

  1. Pandey, S., Phale, P. S., Bhaumik, P. "Structural Modulation of a Periplasmic Sugar-Binding Protein Probes into Its Evolutionary Ancestry." Journal of Structural Biology, 2018, 204(3), 498–506. DOI
  2. Mishra, V., Rathore, I., Arekar, A., Sthanam, L. K., Xiao, H., Kiso, Y., Sen, S., Patankar, S., Gustchina, A., Hidaka, K., Wlodawer, A., Yada, R. Y., Bhaumik, P. "Deciphering the Mechanism of Potent Peptidomimetic Inhibitors Targeting Plasmepsins – Biochemical and Structural Insights." The FEBS Journal, 2018, 285(16), 3077–3096. DOI
  3. Wangchuk, J., Prakash, P., Bhaumik, P., Kondabagil, K. "Bacteriophage N4 Large Terminase: Expression, Purification and X-Ray Crystallographic Analysis." Acta Crystallographica Section F: Structural Biology Communications, 2018, 74(4), 198–204. DOI
  4. Prakash, P., Punekar, N., Bhaumik, P. "Structural Basis for the Catalytic Mechanism and α-Ketoglutarate Cooperativity of Glutamate Dehydrogenase." Journal of Biological Chemistry, 2018, 293(17), 6241-6258. DOI
  5. Kirti, S., Patel, K., Das, S., Shrimali, P., Samanta, S., Kumar, R., Chatterjee, D., Ghosh, D., Kumar, A., Tayalia, P., Maji, S. K. "Amyloid Fibrils with Positive Charge Enhance Retroviral Transduction in Mammalian Cells." ACS Biomaterials Science & Engineering, 2018, 5(1), 126–138. DOI
  6. Mehra, S., Ghosh, D., Kumar, R., Mondal, M., Gadhe, L. G., Das, S., Anoop, A., Jha, N. N., Jacob, R. S., Chatterjee, D., Ray, S., Singh, N., Kumar, A., Maji, S. K. "Glycosaminoglycans Have Variable Effects on α-Synuclein Aggregation and Differentially Affect the Activities of the Resulting Amyloid Fibrils." Journal of Biological Chemistry, 2018, 293(34), 12975–12991. DOI
  7. Sharma, H., John, K., Gaddam, A., Navalkar, A., Maji, S. K., Agrawal, A. "A Magnet-Actuated Biomimetic Device for Isolating Biological Entities in Microwells." Scientific Reports, 2018, 8(1). DOI

2017:

  1. Gaded, V., Anand, R. "Selective Deamination of Mutagens by a Mycobacterial Enzyme." Journal of the American Chemical Society, 2017, 139(31), 10762–10768. DOI
  2. Ray, S., Maitra, A., Biswas, A., Panjikar, S., Mondal, J., Anand, R. "Functional Insights into the Mode of DNA and Ligand Binding of the Tetr Family Regulator Tylp from Streptomyces fradiae." Journal of Biological Chemistry, 2017, 292(37), 15301-15311. DOI
  3. Ghosh, S., Salot, S., Sengupta, S., Navalkar, A., Ghosh, D., Jacob, R., Das, S., Kumar, R., Jha, N. N., Sahay, S., Mehra, S., Mohite, G. M., Ghosh, S. K., Kombrabail, M., Krishnamoorthy, G., Chaudhari, P., Maji, S. K. "P53 Amyloid Formation Leading to Its Loss of Function: Implications in Cancer Pathogenesis." Cell Death & Differentiation, 2017, 24(10), 1784–1798. DOI

2016:

  1. Pandey, S., Modak, A., Phale, P. S., Bhaumik, P. "High Resolution Structures of Periplasmic Glucose-Binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity." Journal of Biological Chemistry, 2016, 291(15), 7844–7857. DOI
  2. Jacob, R. S., Das, S., Ghosh, S., Anoop, A., Jha, N. N., Khan, T., Singru, P., Kumar, A., Maji, S. K. "Amyloid Formation of Growth Hormone in Presence of Zinc: Relevance to Its Storage in Secretory Granules." Scientific Reports, 2016, 6(1). DOI
  3. Jacob, R. S., George, E., Singh, P. K., Salot, S., Anoop, A., Jha, N. N., Sen, S., Maji, S. K. "Cell Adhesion on Amyloid Fibrils Lacking Integrin Recognition Motif." Journal of Biological Chemistry, 2016, 291(10), 5278–5298. DOI