6NLR

Crystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes with trinuclear metals determined by PIXE revealing sulphate ion in active site. Based on PIXE analysis and original date from 3DCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3DCP


Literature

High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.

Grime, G.W.Zeldin, O.B.Snell, M.E.Lowe, E.D.Hunt, J.F.Montelione, G.T.Tong, L.Snell, E.H.Garman, E.F.

(2020) J Am Chem Soc 142: 185-197

  • DOI: 10.1021/jacs.9b09186
  • Primary Citation of Related Structures:  
    6NLR, 6OBY, 6OE2

  • PubMed Abstract: 
  • Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ...

    Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ion beam analysis through particle induced X-ray emission (PIXE), we have quantitatively identified the metal atoms in 30 previously structurally characterized proteins using minimal sample volume and a high-throughput approach. Over half of these metals had been misidentified in the deposited structural models. Some of the PIXE detected metals not seen in the models were explainable as artifacts from promiscuous crystallization reagents. For others, using the correct metal improved the structural models. For multinuclear sites, anomalous diffraction signals enabled the positioning of the correct metals to reveal previously obscured biological information. PIXE is insensitive to the chemical environment, but coupled with experimental diffraction data deposited alongside the structural model it enables validation and potential remediation of metalloprotein models, improving structural and, more importantly, mechanistic knowledge.


    Organizational Affiliation

    Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidinol-phosphataseABC283Listeria monocytogenes serotype 4b str. H7858Mutation(s): 0 
Gene Names: hiskDYZ35_00104
EC: 3.1.3.15
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.278α = 90
b = 191.278β = 90
c = 48.051γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-22
    Changes: Database references