4JET

2.2A resolution structure of Holo hemophore HasA from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Hemophore HasA from Yersinia pestis (HasAyp) Coordinates Hemin with a Single Residue, Tyr75, and with Minimal Conformational Change.

Kumar, R.Lovell, S.Matsumura, H.Battaile, K.P.Moenne-Loccoz, P.Rivera, M.

(2013) Biochemistry 52: 2705-2707

  • DOI: 10.1021/bi400280z
  • Primary Citation of Related Structures:  4JER, 4JES

  • PubMed Abstract: 
  • Hemophores from Serratia marcescens (HasA(sm)) and Pseudomonas aeruginosa (HasA(p)) bind hemin between two loops, which harbor the axial ligands H32 and Y75. Hemin binding to the Y75 loop triggers closing of the H32 loop and enables binding of H32. B ...

    Hemophores from Serratia marcescens (HasA(sm)) and Pseudomonas aeruginosa (HasA(p)) bind hemin between two loops, which harbor the axial ligands H32 and Y75. Hemin binding to the Y75 loop triggers closing of the H32 loop and enables binding of H32. Because Yersinia pestis HasA (HasA(yp)) presents a Gln at position 32, we determined the structures of apo- and holo-HasA(yp). Surprisingly, the Q32 loop in apo-HasA(yp) is already in the closed conformation, but no residue from the Q32 loop binds hemin in holo-HasA(yp). In agreement with the minimal reorganization between the apo- and holo-structures, the hemin on-rate is too fast to detect by conventional stopped-flow measurements.


    Organizational Affiliation

    Center for Bioinformatics, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemophore HasA
A, B, C, D, E, F, G, H, I, J
193Yersinia pestisGene Names: hasA
Find proteins for Q7CL15 (Yersinia pestis)
Go to UniProtKB:  Q7CL15
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.369α = 90.00
b = 69.559β = 100.12
c = 232.317γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
SCALAdata scaling
JDirectordata collection
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: 2013-05-29
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description