4IY8

Bmlp3 - P21 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two Crystal Structures of Bombyx mori Lipoprotein 3 - Structural Characterization of a New 30-kDa Lipoprotein Family Member.

Pietrzyk, A.J.Bujacz, A.Mueller-Dieckmann, J.Lochynska, M.Jaskolski, M.Bujacz, G.

(2013) Plos One 8: e61303-e61303

  • DOI: 10.1371/journal.pone.0061303
  • Primary Citation of Related Structures:  4IY9

  • PubMed Abstract: 
  • The 30-kDa family of lipoproteins from insect hemolymph has been the focus of a number of studies over the last few years. Recently, four crystal structures of Bombyx mori lipoprotein 7 have been determined. Here we report two crystal structures of a ...

    The 30-kDa family of lipoproteins from insect hemolymph has been the focus of a number of studies over the last few years. Recently, four crystal structures of Bombyx mori lipoprotein 7 have been determined. Here we report two crystal structures of another member of the 30-kDa lipoprotein family, Bombyx mori lipoprotein 3 (Bmlp3). The protein was isolated from its natural source, mulberry silkworm hemolymph. It crystallized in two different crystal forms, Bmlp3-p21 (space group P21) and Bmlp3-c2 (space group C2). The crystal structures were solved by molecular replacement using the coordinates of Bmlp7 as a starting model. The crystals of Bmlp3-p21 diffracted X-rays to 2.4 Å resolution and of Bmlp3-c2 to 2.1 Å resolution. Bmlp3 has an overall fold characteristic of 30-kDa lipoproteins, with a VHS-type N-terminal domain and β-trefoil C-terminal domain. Structural comparison of Bmlp3 and Bmlp7 shows that the loops present in the C-terminal domain are flexible and participate in dimer formation. Additionally, new putative binding sites of Bmlp3 have been analyzed in detail and the electrostatic potential of the protein surface at physiological pH 7.4 conditions has been calculated. The results of these calculations are the starting point for an explanation of the recently reported cell-penetrating properties of the 30-kDa lipoproteins.


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30K protein 1
A, B, C, D
239Bombyx moriGene Names: 19G1
Find proteins for Q00802 (Bombyx mori)
Go to UniProtKB:  Q00802
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.930α = 90.00
b = 124.410β = 114.80
c = 67.890γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references