Their father died and left them a shop that is run by some of the heirs; how should the estate be divided among them?

Firstly:

If a person dies and leaves behind a wife, six sons and four
daughters, then the estate is to be divided among the heirs in the following
manner: 

The wife gets one eighth, because there are descendants who
inherit (the sons and daughters of the deceased). Allah, may He be exalted,
says (interpretation of the meaning): “…but
if you leave a child, they [wives] get an eighth of that which you leave…”
[an-Nisa’ 4:12]. 

The rest goes to the children, both males and females, with
each male getting the share of two females, because Allah, may He be
exalted, says (interpretation of the meaning):
“Allah commands you as regards your children’s (inheritance); to the male, a
portion equal to that of two females” [an-Nisa’ 4:12]. 

Secondly: 

If any of the heirs dies before the estate is divided, then
his share of the estate goes to his own heirs. 

Based on that, your sister’s share in the shop that your
father left behind is to be distributed to her heirs, who are in this case: 

The daughter (your sister’s daughter) gets half, because
Allah, may He be exalted, says (interpretation of the meaning):
“…if only one [daughter], her share is half …” [an-Nisa’
4:11]. 

The mother (who is the wife mentioned in the question) gets
one-sixth, because there are descendants who are heirs and some siblings.
Allah (may He be exalted) says (interpretation of the meaning): “For
parents, a sixth share of inheritance to each if the deceased left children;
if no children, and the parents are the (only) heirs, the mother has a
third; if the deceased left brothers or (sisters), the mother has a sixth”
[an-Nisa’ 4:11].

You – the siblings – get the rest, with each male getting the
share of two females. 

If your deceased sister had a husband, he gets one quarter of
what your sister left behind, her daughter gets half and the mother gets
one-sixth, as mentioned above, and the rest goes to the siblings. 

Thirdly: 

With regard to the shop, it is regarded as the property of
all of the heirs; if they wish they may sell it and divide the price between
them, each according to his or her share of inheritance. So the one who
takes one eighth – for example – will take one eighth of the price of the
shop, and so on among the rest of the heirs. 

Or if they wish they may leave the shop to provide them with
income; the one who runs it and looks after it may be given a fixed salary
for that, or he may be given his share of the profit, according to whatever
they agree upon. Then the rest of the profit should be divided among the
heirs, each according to his or her share of inheritance. 

For more information, please see the answer to question no.
193698 

And Allah knows best.