4YYC

Crystal structure of trimethylamine methyltransferase from Sinorhizobium meliloti in complex with unknown ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.139 

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, 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 purificatio ...

    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

    Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative trimethylamine methyltransferase
A
525Rhizobium meliloti (strain 1021)Gene Names: mttB
Find proteins for Q92P20 (Rhizobium meliloti (strain 1021))
Go to UniProtKB:  Q92P20
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 89.162α = 90.00
b = 60.025β = 90.00
c = 88.345γ = 90.00
Software Package:
Software NamePurpose
BLU-MAXdata collection
REFMACrefinement
HKL-3000phasing
PDB_EXTRACTdata extraction
HKL-3000data scaling
Cootmodel building
HKL-3000data reduction
SHELXphasing
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Other
  • Version 1.2: 2016-06-01
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description