4ZNZ

Crystal structure of Escherichia coli carbonic anhydrase (YadF) in complex with Zn - artifact of purification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Protein purification and crystallization artifacts: The tale usually not told.

Niedzialkowska, E.Gasiorowska, O.Handing, K.B.Majorek, K.A.Porebski, P.J.Shabalin, I.G.Zasadzinska, E.Cymborowski, M.Minor, W.

(2016) Protein Sci 25: 720-733

  • DOI: 10.1002/pro.2861
  • Primary Citation of Related Structures:  
    4TNN, 4YYC, 4ZNZ

  • PubMed Abstract: 
  • The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources ...

    The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building.


    Organizational Affiliation

    New York Structural Genomics Research Consortium (NYSGRC), Bronx, New York, 10461.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydraseA220Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: canECBD_3493HO396_00620
EC: 4.2.1.1
UniProt
Find proteins for A0A140NBR3 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140NBR3 
Go to UniProtKB:  A0A140NBR3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.909α = 90
b = 67.909β = 90
c = 84.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000phasing
MLPHAREphasing
SHELXphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54-GM094662

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence