3VOL | pdb_00003vol

X-ray Crystal Structure of PAS-HAMP Aer2 in the CN-bound Form

• PDB DOI: https://doi.org/10.2210/pdb3VOL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-27 Released: 2012-05-23 
• Deposition Author(s): Sawai, H., Sugimoto, H., Shiro, Y., Aono, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.268 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Structural basis for oxygen sensing and signal transduction of the heme-based sensor protein Aer2 from Pseudomonas aeruginosa

Sawai, H., Sugimoto, H., Shiro, Y., Ishikawa, H., Mizutani, Y., Aono, S.

(2012) Chem Commun (Camb) 48: 6523-6525

• PubMed: 22622145 
• DOI: https://doi.org/10.1039/c2cc32549g
• Primary Citation Related Structures: 
  3VOL


• PubMed Abstract: 
  

  The crystal structure of a truncated Aer2, a signal transducer protein from Pseudomonas aeruginosa, consisting of the heme-containing PAS and di-HAMP domains revealed that a distal tryptophan residue (Trp283) plays an important role in stabilizing the heme-bound O(2) and intra-molecular signal transduction upon O(2) binding.

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Organizational Affiliation: 
• Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.44 kDa 
• Atom Count: 1,123 
• Modeled Residue Count: 138 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aerotaxis transducer Aer2	A	233	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: aer2, PA0176
UniProt
Find proteins for Q9I6V6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I6V6  Go to UniProtKB:  Q9I6V6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	C [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.268 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.02	α = 90
b = 83.02	β = 90
c = 107.76	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Sawai, H., Sugimoto, H., Shiro, Y., Aono, S.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations