4PC4

Bombyx mori lipoprotein 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of Bombyx mori lipoprotein 6: comparative structural analysis of the 30-kDa lipoprotein family.

Pietrzyk, A.J.Bujacz, A.ochynska, M.Jaskolski, M.Bujacz, G.

(2014) PLoS One 9: e108761-e108761

  • DOI: 10.1371/journal.pone.0108761
  • Primary Citation of Related Structures:  
    4PC4

  • PubMed Abstract: 
  • The 30-kDa lipoprotein (LP) family of mulberry silkworm comprises major hemolymph proteins specific to the fifth instar larvae. The family consists of 46 members, 24 of which are referred to as typical 30-kDa LPs. To date, two crystal structures of 30-kDa LPs from Bombyx mori have been described (Bmlp3 and Bmlp7) ...

    The 30-kDa lipoprotein (LP) family of mulberry silkworm comprises major hemolymph proteins specific to the fifth instar larvae. The family consists of 46 members, 24 of which are referred to as typical 30-kDa LPs. To date, two crystal structures of 30-kDa LPs from Bombyx mori have been described (Bmlp3 and Bmlp7). Here, we present the crystal structure of Bmlp6, another 30-kDa LP member. Bmlp6 is comprised of two domains characteristic of this family, the VHS-type N-terminal domain and β-trefoil C-terminal domain. The structures of the three 30-kDa LPs have been compared and a number of differences are noted, including loop conformation, the surface electrostatic potential, and the potential binding cavities. We discuss the observed structural differences in the light of the potential different roles of the particular 30-kDa LP members in silkworm physiology.


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, Lodz, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30K lipoproteinA, B, C, D, E245Bombyx moriMutation(s): 0 
UniProt
Find proteins for A7LIK7 (Bombyx mori)
Explore A7LIK7 
Go to UniProtKB:  A7LIK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7LIK7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth B],
M [auth C]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
P [auth C],
Q [auth C],
R [auth C]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.21α = 90
b = 85.75β = 104.84
c = 104.47γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 2.0: 2017-11-22
    Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy