9RLL | pdb_00009rll

Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 
    0.161 (Depositor), 0.161 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.135 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9RLL

This is version 1.2 of the entry. See complete history

Literature

Accurate atomic resolution XFEL structures of a metalloenzyme reveal key insights into its catalytic mechanism.

Rose, S.L.Antonyuk, S.Ferroni, F.M.Sugimoto, H.Yamashita, K.Hirata, K.Ago, H.Ueno, G.Murakami, H.Eady, R.R.Tosha, T.Yamamoto, M.Hasnain, S.S.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70261-1
  • Primary Citation Related Structures: 
    9RLL, 9RN0, 9RNZ, 9RO1, 9ROC, 9ROS

  • PubMed Abstract: 

    Metalloproteins represent a major fraction of the protein kingdom and often exploit the redox chemistry of transition metals to drive key biological events involving proton and electron transfer. Copper is one of the most widely used transition metals whose redox properties are utilised in both electron transfer and catalysis of chemical substrates. Copper nitrite reductases (CuNiRs) utilise two types of copper centres and have become a model system for studying complex biological events that underpin the reaction mechanisms of redox enzymes, including proton-coupled electron transfer and substrate gating. We utilised the higher X-ray energy (13 keV) available at the SACLA X-ray Free Electron Laser (XFEL) and SHELXL refinement to obtain accurate atomic resolution structures of CuNiRs at ~1 Å from three organisms - in the oxidised (low and high pH), reduced and substrate-bound states. A consistent picture now emerges with the observation of a pentacoordinated oxidised catalytic type-2 Cu (T2Cu 2+ ) centre in all cases. A tetracoordinated reduced T2Cu + site with a single solvent ligand has also been captured, giving structural support to the random-sequential scheme with ordered pathway being dominant.


  • Organizational Affiliation
    • Molecular Biophysics Group, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.

Macromolecule Content 

  • Total Structure Weight: 37.42 kDa 
  • Atom Count: 3,200 
  • Modeled Residue Count: 332 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase334Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
UniProt
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25006
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.135 (DCC) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.25α = 90
b = 95.25β = 90
c = 95.25γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



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: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references, Structure summary
  • Version 1.2: 2026-05-06
    Changes: Database references