4FDK | pdb_00004fdk

F78L Tt H-NOX

• PDB DOI: https://doi.org/10.2210/pdb4FDK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-28 Released: 2013-08-28 
• Deposition Author(s): Weinert, E.E., Phillips-Piro, C.M., Marletta, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Porphyrin pi-stacking in a heme protein scaffold tunes gas ligand affinity.

Weinert, E.E., Phillips-Piro, C.M., Marletta, M.A.

(2013) J Inorg Biochem 127C: 7-12

• PubMed: 23831583 
• DOI: https://doi.org/10.1016/j.jinorgbio.2013.06.004
• Primary Citation Related Structures: 
  4FDK


• PubMed Abstract: 
  

  The role of π-stacking in controlling redox and ligand binding properties of porphyrins has been of interest for many years. The recent discovery of H-NOX domains has provided a model system to investigate the role of porphyrin π-stacking within a heme protein scaffold. Removal of a phenylalanine-porphyrin π-stack dramatically increased O2, NO, and CO affinities and caused changes in redox potential (~40mV) without any structural changes. These results suggest that small changes in redox potential affect ligand affinity and that π-stacking may provide a novel route to engineer heme protein properties for new functions.

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Organizational Affiliation: 
• Department of Chemistry, Emory University, Atlanta, GA 30322, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.32 kDa 
• Atom Count: 3,492 
• Modeled Residue Count: 376 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting chemotaxis protein	A, B	188	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 1  Gene Names: Tar4, TTE0680
UniProt
Find proteins for Q8RBX6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBX6  Go to UniProtKB:  Q8RBX6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OXY	D [auth A], F [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.552	α = 90
b = 127.426	β = 90
c = 42.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
ELVES	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Weinert, E.E., Phillips-Piro, C.M., Marletta, M.A.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description