1JJW | pdb_00001jjw

Structure of Haemophilus influenzae HslV Protein at 1.9 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb1JJW/pdb

• Classification: HYDROLASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2001-07-09 Released: 2001-12-05 
• Deposition Author(s): Sousa, M.C., McKay, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.249 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site.

Sousa, M.C., McKay, D.B.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1950-1954

• PubMed: 11717526 
• DOI: https://doi.org/10.1107/s090744490101575x
• Primary Citation Related Structures: 
  1JJW


• PubMed Abstract: 
  

  The structure of the Haemophilus influenzae HslV protease of the HslUV 'prokaryotic proteasome' has been solved by molecular replacement and refined with data to 1.9 A resolution. The protease is a 'double donut' of hexameric rings; two alternative sets of intermolecular interactions between protomers in the rings result in 'quasi-equivalent' packing within the assembly. Anomalous scattering data from crystals with potassium present in the mother liquor reveal a K(+) ion bound with octahedral coordination near the active-site Thr1 residue. The site also binds Na(+) ions and is likely to bind Mg(2+), suggesting that monovalent and divalent metal ions may influence the catalytic activity of the protease.

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Organizational Affiliation: 
• Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.83 kDa 
• Atom Count: 4,040 
• Modeled Residue Count: 519 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-DEPENDENT PROTEASE HSLV	A, B, C	174	Haemophilus influenzae	Mutation(s): 0  Gene Names: HslV EC: 3.4.99 (PDB Primary Data), 3.4.25.2 (UniProt)
UniProt
Find proteins for P43772 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43772  Go to UniProtKB:  P43772

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	D [auth A], E [auth B], F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.249 (Depositor) 
• R-Value Work:  0.215 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.893	α = 90
b = 122.331	β = 90
c = 126.288	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-05 
Deposition Author(s): Sousa, M.C., McKay, D.B.

Revision History  

• Version 1.0: 2001-12-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description