3MOR | pdb_00003mor

Crystal structure of Cathepsin B from Trypanosoma Brucei

• PDB DOI: https://doi.org/10.2210/pdb3MOR/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma brucei
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-04-23 Released: 2011-11-02 
• Deposition Author(s): Cupelli, K., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

In vivo protein crystallization opens new routes in structural biology.

Koopmann, R., Cupelli, K., Redecke, L., Nass, K., Deponte, D.P., White, T.A., Stellato, F., Rehders, D., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M.J., Bostedt, C., Boutet, S., Bozek, J.D., Caleman, C., Coppola, N., Davidsson, J., Doak, R.B., Ekeberg, T., Epp, S.W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C.Y., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Hunter, M.S., Kassemeyer, S., Kirian, R.A., Lomb, L., Maia, F.R., Kimmel, N., Martin, A.V., Messerschmidt, M., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M.M., Shoeman, R.L., Sierra, R.G., Soltau, H., Stern, S., Struder, L., Timneanu, N., Ullrich, J., Wang, X., Weidenspointner, G., Weierstall, U., Williams, G.J., Wunderer, C.B., Fromme, P., Spence, J.C., Stehle, T., Chapman, H.N., Betzel, C., Duszenko, M.

(2012) Nat Methods 9: 259-262

• PubMed: 22286384 
• DOI: https://doi.org/10.1038/nmeth.1859
• Primary Citation Related Structures: 
  3MOR


• PubMed Abstract: 
  

  Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

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Organizational Affiliation: 
• Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.25 kDa 
• Atom Count: 4,158 
• Modeled Residue Count: 520 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B-like cysteine protease	A, B	317	Trypanosoma brucei	Mutation(s): 0  Gene Names: Tb927.6.560 EC: 3.4.22
UniProt
Find proteins for Q6R7Z5 (Trypanosoma brucei) Explore Q6R7Z5  Go to UniProtKB:  Q6R7Z5
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.91	α = 90
b = 75.49	β = 104.8
c = 75.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Cupelli, K., Stehle, T.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary