1EWF

THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold.

Kleiger, G.Beamer, L.J.Grothe, R.Mallick, P.Eisenberg, D.

(2000) J.Mol.Biol. 299: 1019-1034

  • DOI: 10.1006/jmbi.2000.3805

  • PubMed Abstract: 
  • We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of t ...

    We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of the two domains, we compare the corresponding residue positions in the two domains by the method of 3D-1D profiles. A 3D-1D profile is a string formed by assigning each position in the 3D structure to one of 18 environment classes. The environment classes are defined by the local secondary structure, the area of the residue which is buried from solvent, and the fraction of the area buried by polar atoms. A structural alignment between the two BPI domains was used to compare the 3D-1D environments of structurally equivalent positions. Greater than 31% of the aligned positions have conserved 3D-1D environments, but only 13% have conserved residue identities. Analysis of the 3D-1D environmentally conserved positions helps to identify pairs of residues likely to be important in conserving the fold, regardless of the residue similarity. We find examples of 3D-1D environmentally conserved positions with dissimilar residues which nevertheless play similar structural roles. To generalize our findings, we analyzed four other proteins with similar structures yet dissimilar sequences. Together, these examples show that aligned pairs of dissimilar residues often share similar structural roles, stabilizing dissimilar sequences in the same fold.


    Related Citations: 
    • Crystal Structure of Human BPI and Two Bound Phospholipids at 2.4 Angstrom Resolution
      Beamer, L.J.,Carroll, S.F.,Eisenberg, D.
      (1997) Science 276: 1861


    Organizational Affiliation

    UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, Los Angeles, CA, 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
A
456Homo sapiensMutation(s): 1 
Gene Names: BPI
Find proteins for P17213 (Homo sapiens)
Go to Gene View: BPI
Go to UniProtKB:  P17213
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download SDF File 
Download CCD File 
A
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.320α = 90.00
b = 31.230β = 103.20
c = 80.660γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Database references
  • Version 1.4: 2018-01-31
    Type: Experimental preparation