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Protein Crystallography (BL-21) [an error occurred while processing this directive]

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Protein Crystallography

Overview

The protein crystallography (PX-BL21) beamline is installed on 1.5 Tesla bending magnet source (port no. 21; 10o port) of Indus-2 synchrotron. This beamline has been designed for macromolecular crystallography i.e. diffraction studies on single crystals of protein, DNA and their complexes. It has also been designed to perform high-pressure studies using single crystal and powder diffraction experiments. The beamline can be tuned to desired energy in the range between 5 to 20 keV (with bandwidth of ~1 eV) corresponding to wavelength of 2.48– 0.62 Å. The beamline is equipped to perform Single- and Multi- wavelength anomalous diffraction experiments (SAD, MAD) by fine-tuning energy of beam with required energy resolution. The typical time for data acquisition is about 10 to 60 sec per frame depending on the crystal quality and synchrotron beam current. The beamline is associated with a well-equipped biochemical laboratory and cold rooms to grow, cryo-soak and cryo-freeze the protein crystals.
Protein Crystallography Beamline (PX-BL21), Indus-2, RRCAT, Indore, Madhya Pradesh, PIN 452013, India

Beamline details

Beamline name PX-BL21
Source type 1.5 T bending magnet (2.5 GeV, ~ 200 mA Indus-2)
Mirrors Both CM and TM are 1.2 m single-crystal Si with Rh coating
Monochromator Water-cooled DCM with Si (111) or Si(220) crystals
Energy range (keV) 5-20
Wavelength range (A° ) 0.62–2.48
Beam size (m) (FWHM) 500 x 500
Flux (photons s-1) * 1.2 x 1010

Schematic of PX-beamline (BL21)
 

Schematic of PX-BL21 beamline

Experimental station & other details

Experiments MONOCHROMATIC, SAD, MAD
Experimental stage MARdtb
Goniometer single axis
Detector type CCD
Detector MARCCD 225 (Rayonix), 225mm x 225mm (active area)
Detector resolution 3072 * 3072 pixels; pixel size: 73 x 73 μm2
Detector saturation counts 60,000 photons/pixel
Detector angular displacement (2θ) 0–30o
Fluorescence detector AMPTEK XR 100 SDD
Cryo sample cooler Oxford Cryostream - 700 series
Cryogenic Robotic sample changer Carousel of 19 samples (MAR research)
Biochem Lab Facility Full-fledged working laboratory with cold rooms
Cryo-pins recommended SPINE
On-site data processing server HP Z800 (12-core Xeon 2.67 GHz, 24 GB RAM)
Software Automar, XDS, Mosflm, CCP4, PHENIX, Coot, Pymol


Setup Image Flow Chart

How to apply for beam-time at PX-BL21 ?

The beam-time is allotted to users through an online portal (https://www.info-rrcat.ernet.in/beamline/). However, it is requested to users (prior to online application) to send an email to the contacts (given below) for knowing the availability of the beamline/synchrotron with the proposed dates of their experiments. Users are requested to arrange their travel only after they receive the confirmation from the beamline team.

How to acknowledge the use of the beamline?

The use of PX-BL21 for data collection and/or testing of the crystals is requested to be acknowledged by both, a) citing the beamline paper, and b) using the following phrase in the acknowledgement "PX-BL21 beamline (BARC) at Indus-2, RRCAT, Indore".

Beamline paper: Ashwani Kumar, Biplab Ghosh, H. K. Poswal, K. K. Pandey, Jagannath, M. V. Hosur, Abhilash Dwivedi, Ravindra D. Makde and Surinder M. Sharma, "Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron, J. Synchrotron Rad. (2016). 23, 629-634. doi: http://dx.doi.org/10.1107/S160057751600076X

Biochemical & crystallization facility

The PX beamline is associated with a well-equipped biochemical laboratory and cold rooms. This laboratory has all the necessary infrastructure and facility for protein expression, purification and crystallization. It also has dedicated crystal growth rooms, incubators and microscopes. The users may carry out necessary post-crystallization soaks and crystal freezing using this facility. There is a LN2 deware to store and maintain the crystals under the liquid nitrogen temperature.
Biochem  & crystallization facility

PDB depositions (Total >39 Nos)

3X1J, 3X1K, 3X1M, 4Q22, 4QG5, 4R42, 4R60, 4RUK, 4WL2, 4WL3, 4WRZ, 4WS2, 4WS3, 4WS4, 4WS6, 5AQD, 5C82, 5CDE, 5CDL, 5CDV, 5CE6, 5CIK, 5CNW, 5CNX, 5CO3, 5CP1, 5EMH, 5FCF, 5FCH, 5FVB, 5GGX, 5GGY, 5GIQ, 5GIU, 5GIV, 5GUI, 5IQZ, 5KHL, 5X49

Selected Publications

  1. Mathur S, Deshmukh P, Tripathi S, Marimuthu P, Padmanabhan B.
    Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and heoretical studies on phenanthridinone analogs.
    J Biomol Struct Dyn. 2017 Jul 31:1-19.

  2. Bihani SC, Panicker L, Rajpurohit YS, Misra HS, Kumar V.
    drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases.
    Antioxid Redox Signal. 2017 Oct 16. doi: 10.1089/ars.2016.6960.

  3. Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG.
    Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.
    FEBS J. 2017 Oct 7. doi: 10.1111/febs.14289

  4. Are VN, Jamdar SN, Ghosh B, Goyal VD, Kumar A, Neema S, Gadre R, Makde RD.
    Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.
    Proteins. 2017 Sep 20. doi: 10.1002/prot.25389.

  5. Sharma B, Jamdar SN, Ghosh B, Yadav P, Kumar A, Kundu S, Goyal VD, Makde RD.
    Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations.
    Biochim Biophys Acta. 2017 pii: S1570-9639(17)30201-7. doi: 10.1016/j.bbapap.2017.07.023.

  6. Shivakumar KI, Swathi K, Patil G, Das T, Kumar A, Makde RD, Vanka K, Babu SS, Narayan KS, Sanjayan GJ.
    Mixed-Stack Charge Transfer Crystals of Pillar[5]quinone and Tetrathiafulvalene Exhibiting Ferroelectric Features.
    Chemistry. 2017 doi: 10.1002/chem.201702577.

  7. Singh R, Jamdar SN, Goyal VD, Kumar A, Ghosh B, Makde RD.
    Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes.
    J Biol Chem. 2017 Jun 16;292(24):10035-10047

  8. Mohapatra C, Kumar Jagdev M, Vasudevan D.
    Crystal structures reveal N-terminal Domain of Arabidopsis thaliana ClpD to be highly divergent from that of ClpC1.
    Sci Rep. 2017;7:44366.

  9. Agarwal S, Dey S, Ghosh B, Biswas M, Dasgupta J.
    Structure and dynamics of Type III periplasmic proteins VcFhuD and VcHutB reveal molecular basis of their distinctive ligand binding properties.
    Sci Rep. 2017;7:42812.

  10. Are VN, Kumar A, Kumar S, Goyal VD, Ghosh B, Bhatnagar D, Jamdar SN, Makde RD.
    Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.
    Biochim Biophys Acta. 2017;1865(2):153-164.

  11. Priyanka A, Solanki V, Parkesh R, Thakur KG.
    Crystal structure of the N-terminal domain of human SIRT7 reveals a three-helical domain architecture.
    Proteins. 2016;84(10):1558-63

  12. Roy A, Reddi R, Sawhney B, Ghosh DK, Addlagatta A, Ranjan A.
    Expression, Functional Characterization and X-ray Analysis of HosA, A Member of MarR Family of Transcription Regulator from Uropathogenic Escherichia coli.
    Protein J. 2016 Aug;35(4):269-82.

  13. Kumar V, Sonani RR, Sharma M, Gupta GD, Madamwar D.
    Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM.
    Photosynth Res. 2016;129(1):17-28

  14. Chatterjee R, Mondal A, Basu A, Datta S.
    Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa.
    Biochim Biophys Acta. 2016;1864(7):773-86.

  15. Are VN, Ghosh B, Kumar A, Gadre R, Makde RD.
    Crystal structure and dynamics of Spt16N-domain of FACT complex from Cicer arietinum.
    Int J Biol Macromol. 2016 ;88:36-43.

  16. Bihani SC, Chakravarty D, Ballal A. KatB,
    a cyanobacterial Mn-catalase with unique active site configuration: Implications for enzyme function.
    Free Radic Biol Med. 2016;93:118-29

  17. Avinash VS, Panigrahi P, Chand D, Pundle A, Suresh CG, Ramasamy S.
    Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity.
    J Struct Biol. 2016 ;193(2):85-94.

  18. Ghosh B, Goyal VD.
    Gating role of His 72 in TmPurL enzyme uncovered by structural analyses and molecular dynamics simulations.
    Bioorg Med Chem Lett. 2016 Dec 1;26(23):5644-5649.

  19. Waugh B, Sen U, Banerjee R.
    Crystal structure of phosphoglucomutase from Leishmania major at 3.5 Å resolution.
    Biochimie. 2016;121:102-11.

  20. Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M.
    Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications.
    Acta Crystallogr D Biol Crystallogr. 2015;71(Pt 7):1514-27.

  21. Kumar A, Ghosh B, Poswal HK, Pandey KK; Jagannath, Hosur MV, Dwivedi A, Makde RD, Sharma SM.
    Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron.
    J Synchrotron Radiat. 2016 Mar;23(2):629-34.

  22. Jamdar SN, Are VN, Navamani M, Kumar S, Nagar V, Makde RD.
    The members of M20D peptidase subfamily from Burkholderia cepacia, Deinococcus radiodurans and Staphylococcus aureus (HmrA) are carboxydipeptidases, primarily specific for Met-X dipeptides.
    Arch Biochem Biophys. 2015 Dec 1;587:18-30.

PX-BL21 users

Contacts

  • Dr. Ashwani Kumar
    Phone: +91-731-244-2116
    ashwani(at)rrcat.gov.in

  • Dr. Biplab Ghosh
    Phone: +91-731-244-2116
    biplab(at)rrcat.gov.in

  • Dr. Ravindra D. Makde
    Phone: +91-731-244-2175
    ravimakde(at)rrcat.gov.in

  • Beamline phone number: +91-731-244-2521

Photo Gallery

Protein Crystallography beamline, Indus-2, Indore A view of beamline showing critical beamline componenets from the front end side
Dr. Ajit Bikram (Bose institute, Kolkata) and his students are collecting diffraction data at PX-BL21 beamline Experimental fluorescence spectrum from a selenomethionine protein crystal measured at the Se K-edge. Inset: the anomalous scattering factors (f' and f") are calculated from the experimental fluorescence data using the program CHOOCH.
Anomalous difference Fourier map, contoured at 5.0 sigma and superposed on the structure of Xaa-Pro peptidase from Deinococcus radiodurans (PDB entry, 5CDL). Anomalous difference Fourier map, contoured at 5.0 sigma and superposed on the structure of the active site of Xaa-Pro dipeptidase from Xanthomonas campestris, showing two zinc ions (PDB entry, 5CDE).
Some structures from PX-BL21 beamline
Last Modification on: November 2017