Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38324.68 
• Atom Count: 2453 
• Residue Count: 340 
• Unique protein chains: 1

4HWY

Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography

• DOI: 10.2210/pdb4HWY/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
• Expression System: Spodoptera frugiperda


• Deposited: 2012-11-09 Released: 2012-12-05 
• Deposition Author(s): Redecke, L., Nass, K., DePonte, D.P., White, T.A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T.R.M., Boutet, S., Williams, G.W., Messerschmidt, M., Seibert, M.M., Aquila, A., Arnlund, D., Bajt, S., Barth, T., Bogan, M.J., Caleman, C., Chao, T.-C., Doak, R.B., Fleckenstein, H., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M.S., Johansson, L.C., Kassemeyer, S., Katona, G., Kirian, R.A., Koopmann, R., Kupitz, C., Lomb, L., Martin, A.V., Mogk, S., Neutze, R., Shoemann, R.L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N.A., Spence, J.C.H., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 

Literature

Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.

Redecke, L., Nass, K., DePonte, D.P., White, T.A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T.R., Boutet, S., Williams, G.J., Messerschmidt, M., Seibert, M.M., Aquila, A., Arnlund, D., Bajt, S., Barth, T., Bogan, M.J., Caleman, C., Chao, T.C., Doak, R.B., Fleckenstein, H., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M.S., Johansson, L.C., Kassemeyer, S., Katona, G., Kirian, R.A., Koopmann, R., Kupitz, C., Lomb, L., Martin, A.V., Mogk, S., Neutze, R., Shoeman, R.L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N.A., Spence, J.C., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H.N.

(2013) Science 339: 227-230

• PubMed: 23196907 
• DOI: 10.1126/science.1229663


• PubMed Abstract: 
  

The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.

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Organizational Affiliation: 

Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cysteine peptidase C (CPC)	A	340	Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
Find proteins for D6XHE1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Go to UniProtKB:  D6XHE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 125.400	α = 90.00
b = 125.400	β = 90.00
c = 54.560	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
CrystFEL	data reduction
CXI	data collection
REFMAC	refinement
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-09 
• Released Date: 2012-12-05 
• Deposition Author(s): Redecke, L., Nass, K., DePonte, D.P., White, T.A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T.R.M., Boutet, S., Williams, G.W., Messerschmidt, M., Seibert, M.M., Aquila, A., Arnlund, D., Bajt, S., Barth, T., Bogan, M.J., Caleman, C., Chao, T.-C., Doak, R.B., Fleckenstein, H., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M.S., Johansson, L.C., Kassemeyer, S., Katona, G., Kirian, R.A., Koopmann, R., Kupitz, C., Lomb, L., Martin, A.V., Mogk, S., Neutze, R., Shoemann, R.L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N.A., Spence, J.C.H., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H.

Revision History 

• Version 1.0: 2012-12-05
  Type: Initial release
• Version 1.1: 2012-12-19
  Type: Database references
• Version 1.2: 2013-01-23
  Type: Database references
• Version 1.3: 2016-12-21
  Type: Data collection
• Version 1.4: 2017-11-15
  Type: Advisory, Data collection
• Version 1.5: 2018-02-14
  Type: Data collection, Source and taxonomy