6OBY

The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 

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: 

  • 3KB1 - determined by Forouhar, F., Lew, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)  

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:  

  • 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

    Materials Design and Innovation , SUNY Buffalo , 700 Ellicott St. , Buffalo , New York 14203 , United States.,Hauptman-Woodward Medical Research Institute , 700 Ellicott St. , Buffalo , New York 14203 , United States.,Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom.,Department of Biological Sciences , Columbia University , New York , New York 10027 , United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences , Rensselaer Polytechnic Institute , Troy New York 12180 United States.,Ion Beam Centre, Advanced Technology Institute , University of Surrey , Guildford, Surrey GU2 7XH , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron-sulfur cluster carrier protein
A, B
262Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Find proteins for O28015 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O28015
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.440α = 90.00
b = 67.682β = 90.09
c = 79.403γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXDEphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Author supporting evidence
  • Version 1.2: 2020-01-22
    Type: Database references