6ZAW

Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.

Rose, S.L.Antonyuk, S.V.Sasaki, D.Yamashita, K.Hirata, K.Ueno, G.Ago, H.Eady, R.R.Tosha, T.Yamamoto, M.Hasnain, S.S.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd8523
  • Primary Citation of Related Structures:  
    6ZAR, 6ZAS, 6ZAT, 6ZAU, 6ZAV, 6ZAW, 6ZAX

  • PubMed Abstract: 

    Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR ( Br 2D NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue ( Ax NiR) and green ( Ac NiR) subclasses, Br 2D NiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.


  • Organizational Affiliation

    Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase347Bradyrhizobium sp. ORS 375Mutation(s): 0 
Gene Names: nirKBRAO375_4030011
EC: 1.7.2.1
UniProt
Find proteins for H0SLX7 (Bradyrhizobium sp. (strain ORS 375))
Explore H0SLX7 
Go to UniProtKB:  H0SLX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH0SLX7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
B, C, D
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
L [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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M [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO (Subject of Investigation/LOI)
Query on NO

Download Ideal Coordinates CCD File 
N [auth A]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.87α = 90
b = 106.87β = 90
c = 106.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N013972/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description