6GB8

Copper nitrite reductase from Achromobacter cycloclastes: small cell polymorph dataset 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography.

Ebrahim, A.Appleby, M.V.Axford, D.Beale, J.Moreno-Chicano, T.Sherrell, D.A.Strange, R.W.Hough, M.A.Owen, R.L.

(2019) Acta Crystallogr D Struct Biol 75: 151-159

  • DOI: 10.1107/S2059798318010240
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However ...

    The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However, the combination of crystal-to-crystal variation and X-ray-induced changes can make the formation of a final complete data set challenging; this is particularly true in the case of metalloproteins, where X-ray-induced changes occur rapidly and at the active site. An approach is described that allows the resolution, separation and structure determination of crystal polymorphs, and the tracking of radiation damage in microcrystals. Within the microcrystal population of copper nitrite reductase, two polymorphs with different unit-cell sizes were successfully separated to determine two independent structures, and an X-ray-driven change between these polymorphs was followed. This was achieved through the determination of multiple serial structures from microcrystals using a high-throughput high-speed fixed-target approach coupled with robust data processing.


    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 reductase
A
340Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Go to UniProtKB:  P25006
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO2
Query on NO2

Download SDF File 
Download CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 96.382α = 90.00
b = 96.382β = 90.00
c = 96.382γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
DIALSdata scaling
REFMACrefinement
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M022714/1
Leverhulme TrustUnited KingdomRPG-2014-355

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references