Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 36.82 kDa 
• Atom Count: 3029 
• Modelled Residue Count: 332 
• Deposited Residue Count: 332 
• Unique protein chains: 1

5I6N

Crystal Structure of Copper Nitrite Reductase at 100K after 11.73 MGy

• PDB DOI: 10.2210/pdb5I6N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter cycloclastes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-16 Released: 2016-07-13 
• Deposition Author(s): Horrell, S., Hough, M.A., Strange, R.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.165 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 

Literature

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

Horrell, S., Antonyuk, S.V., Eady, R.R., Hasnain, S.S., Hough, M.A., Strange, R.W.

(2016) IUCrJ 3: 271-281

• PubMed: 27437114 
• DOI: 10.1107/S205225251600823X
• Primary Citation of Related Structures:  
  5I6K, 5I6L, 5I6M, 5I6N, 5I6O, 5I6P


• PubMed Abstract: 
  

Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

---

Organizational Affiliation: 

School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	332	Achromobacter cycloclastes	Mutation(s): 0  Gene Names: nirK EC: 1.7.2.1
UniProt
Find proteins for P25006 (Achromobacter cycloclastes) Explore P25006  Go to UniProtKB:  P25006

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M
NO	D [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYAM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.165 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.192	α = 90
b = 95.192	β = 90
c = 95.192	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-16 
• Released Date: 2016-07-13 
Deposition Author(s): Horrell, S., Hough, M.A., Strange, R.W.

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2016-09-21
  Changes: Database references
• Version 1.3: 2016-09-28
  Changes: Database references