5IXR | pdb_00005ixr

Crystal Structure of C139A nostoc H-NOX domain with imidazole

• PDB DOI: https://doi.org/10.2210/pdb5IXR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-23 Released: 2017-08-09 
• Deposition Author(s): Kumar, V., van den Akker, F.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of C139A nostoc H-NOX domain with imidazole

Kumar, V., van den Akker, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.29 kDa 
• Atom Count: 3,026 
• Modeled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alr2278 protein	A, B	182	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 1  Gene Names: alr2278
UniProt
Find proteins for A0ACD6B960 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore A0ACD6B960  Go to UniProtKB:  A0ACD6B960

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MLI	E [auth A], H [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
IMD	D [auth A], G [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.051	α = 90
b = 123.051	β = 90
c = 123.051	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Kumar, V., van den Akker, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01 HL075329

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description