1WXR | pdb_00001wxr

Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1WXR/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2005-01-31 Released: 2005-03-01 
• Deposition Author(s): Otto, B.R., Sijbrandi, R., Luirink, J., Oudega, B., Heddle, J.G., Mizutani, K., Park, S.-Y., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.243 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli

Otto, B.R., Sijbrandi, R., Luirink, J., Oudega, B., Heddle, J.G., Mizutani, K., Park, S.-Y., Tame, J.R.H.

(2005) J Biological Chem 280: 17339-17345

• PubMed: 15728184 
• DOI: https://doi.org/10.1074/jbc.M412885200
• Primary Citation Related Structures: 
  1WXR


• PubMed Abstract: 
  

  The acquisition of iron is essential for the survival of pathogenic bacteria, which have consequently evolved a wide variety of uptake systems to extract iron and heme from host proteins such as hemoglobin. Hemoglobin protease (Hbp) was discovered as a factor involved in the symbiosis of pathogenic Escherichia coli and Bacteroides fragilis, which cause intra-abdominal abscesses. Released from E. coli, this serine protease autotransporter degrades hemoglobin and delivers heme to both bacterial species. The crystal structure of the complete passenger domain of Hbp (110 kDa) is presented, which is the first structure from this class of serine proteases and the largest parallel beta-helical structure yet solved.

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Organizational Affiliation: 
• Department of Molecular Microbiology, Faculty of Earth and Life Sciences, Vrije Universiteit de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 111.96 kDa 
• Atom Count: 8,197 
• Modeled Residue Count: 1,035 
• Deposited Residue Count: 1,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
haemoglobin protease	A	1,048	Escherichia coli	Mutation(s): 0  Gene Names: HBP EC: 3.4.21 Membrane Entity: Yes
UniProt
Find proteins for O88093 (Escherichia coli) Explore O88093  Go to UniProtKB:  O88093

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.243 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.028	α = 90
b = 115.028	β = 90
c = 437.057	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Otto, B.R., Sijbrandi, R., Luirink, J., Oudega, B., Heddle, J.G., Mizutani, K., Park, S.-Y., Tame, J.R.H.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references