Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 23.01 kDa 
• Atom Count: 1719 
• Residue Count: 193 
• Unique protein chains: 1

4TNN

Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.

• DOI: 10.2210/pdb4TNN/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli str. K-12 substr. MC4100
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-04 Released: 2014-06-25 
• Deposition Author(s): Gasiorowska, O.A., Cymborowski, M.T., Handing, K.B., Shabalin, I.G., Zasadzinska, E., Niedzialkowska, E., Porebski, P.J., Minor, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.215 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

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

• PubMed: 26660914 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding lipocalin	A	193	Escherichia coli str. K-12 substr. MC4100	Mutation(s): 0  Gene Names: yodA, BN896_1774

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.215 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 3₁ 2 1
• Diffraction Data DOI: 10.18430/m31g6b Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.583	α = 90
b = 76.583	β = 90
c = 61.944	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXDE	phasing
MLPHARE	phasing
DM	phasing
Coot	model building
PDB_EXTRACT	data extraction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-06-04 
• Released Date: 2014-06-25 
Deposition Author(s): Gasiorowska, O.A., Cymborowski, M.T., Handing, K.B., Shabalin, I.G., Zasadzinska, E., Niedzialkowska, E., Porebski, P.J., Minor, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM053163

Revision History 

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Refinement description
• Version 1.2: 2017-04-19
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence