Crystal structure of encapsulin from Mycolicibacterium hassiacum

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation.

Loncar, N.Rozeboom, H.J.Franken, L.E.Stuart, M.C.A.Fraaije, M.W.

(2020) Biochem Biophys Res Commun 529: 548-553

  • DOI: https://doi.org/10.1016/j.bbrc.2020.06.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Using a newly discovered encapsulin from Mycolicibacterium hassiacum, several biocatalysts were packaged in this robust protein cage. The encapsulin was found to be easy to produce as recombinant protein. Elucidation of its crystal structure revealed that it is a spherical protein cage of 60 protomers (diameter of 23 nm) with narrow pores. By developing an effective coexpression and isolation procedure, the effect of packaging a variety of biocatalysts could be evaluated. It was shown that encapsulation results in a significantly higher stability of the biocatalysts. Most of the targeted cofactor-containing biocatalysts remained active in the encapsulin. Due to the restricted diameters of the encapsulin pores (5-9 Å), the protein cage protects the encapsulated enzymes from bulky compounds. The work shows that encapsulins may be valuable tools to tune the properties of biocatalysts such as stability and substrate specificity.

  • Organizational Affiliation

    GECCO Biotech, Nijenborgh 4, 9747AG, Groningen, the Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
265Mycolicibacterium hassiacum DSM 44199Mutation(s): 0 
Gene Names: linC731_3737
EC: 3.4
Find proteins for K5BEG2 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849))
Explore K5BEG2 
Go to UniProtKB:  K5BEG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK5BEG2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth E]
AC [auth H]
AD [auth K]
AE [auth O]
AA [auth B],
AB [auth E],
AC [auth H],
AD [auth K],
AE [auth O],
BA [auth B],
BB [auth E],
BC [auth H],
BD [auth K],
BE [auth O],
CA [auth B],
CB [auth E],
CC [auth H],
CD [auth L],
CE [auth O],
DA [auth B],
DB [auth E],
DC [auth H],
DD [auth L],
DE [auth O],
EA [auth B],
EB [auth E],
EC [auth H],
ED [auth L],
EE [auth O],
FA [auth C],
FB [auth F],
FC [auth H],
FD [auth L],
FE [auth O],
GA [auth C],
GB [auth F],
GC [auth H],
GD [auth L],
HA [auth C],
HB [auth F],
HC [auth H],
HD [auth L],
IA [auth C],
IB [auth F],
IC [auth H],
ID [auth L],
JA [auth C],
JB [auth F],
JC [auth I],
KA [auth C],
KB [auth F],
KC [auth I],
KD [auth M],
LA [auth C],
LB [auth F],
LC [auth I],
LD [auth M],
MA [auth C],
MB [auth F],
MC [auth I],
MD [auth M],
NA [auth C],
NC [auth I],
ND [auth M],
OA [auth C],
OB [auth G],
OC [auth J],
OD [auth M],
P [auth A],
PB [auth G],
PC [auth J],
PD [auth M],
Q [auth A],
QA [auth D],
QB [auth G],
QC [auth J],
QD [auth M],
R [auth A],
RA [auth D],
RB [auth G],
RC [auth J],
RD [auth N],
S [auth A],
SA [auth D],
SB [auth G],
SC [auth J],
SD [auth N],
T [auth A],
TA [auth D],
TB [auth G],
TC [auth J],
TD [auth N],
U [auth A],
UA [auth D],
UB [auth G],
UC [auth J],
UD [auth N],
V [auth A],
VA [auth D],
VB [auth G],
VC [auth K],
VD [auth N],
W [auth A],
WA [auth D],
WB [auth G],
WC [auth K],
WD [auth N],
X [auth B],
XA [auth E],
XB [auth G],
XC [auth K],
XD [auth N],
Y [auth B],
YA [auth E],
YB [auth G],
YC [auth K],
Z [auth B],
ZA [auth E],
ZB [auth H],
ZC [auth K],
ZD [auth O]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
JD [auth L],
NB [auth F],
PA [auth C],
YD [auth N]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.272α = 90
b = 242.149β = 90
c = 271.557γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-08-12
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description