5I6N

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


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 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1107/S205225251600823X
  • Structures With Same Primary Citation

  • 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- ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-containing nitrite reductaseA332Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

Download CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
NO
Query on NO

Download CCD File 
A
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
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 = 95.192α = 90
b = 95.192β = 90
c = 95.192γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

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