6MX5 | pdb_00006mx5

Crystal structure of H-NOX protein from Nostoc sp.

• PDB DOI: https://doi.org/10.2210/pdb6MX5/pdb
• Entry: 6MX5 supersedes: 6DX6

• Classification: SIGNALING PROTEIN
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-30 Released: 2018-11-07 
• Deposition Author(s): Weichsel, A., Kievenaar, J.A., Montfort, W.R.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structure of H-NOX domain from cyanobacteria Nostoc sp

Kievenaar, J.A., Croft, J.T., Li, J., Feng, C., Weichsel, A., Montfort, W.R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 21.93 kDa 
• Atom Count: 1,553 
• Modeled Residue Count: 189 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alr2278 protein	A	190	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: alr2278

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.169	α = 90
b = 65.169	β = 90
c = 103.264	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Weichsel, A., Kievenaar, J.A., Montfort, W.R.
• This entry supersedes: 6DX6

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM117357
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P30 CA023074
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	T32 GM008804
American Heart Association	United States	14GRNT20080006
American Heart Association	United States	16PRE31090034

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description