6OE2

X-Ray Structure of the C-terminal domain (277-440) of Putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR324A. Re-refinement of 3GGL with correct metal Mn replacing Zn. New metal confirmed with PIXE analysis of original sample.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

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


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: https://doi.org/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 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

    Ion Beam Centre, Advanced Technology Institute , University of Surrey , Guildford, Surrey GU2 7XH , United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitobiase169Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: nagJ_1ERS852430_00185SAMN02910322_00414
EC: 3.2.1.169
UniProt
Find proteins for Q8A9F0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A9F0 
Go to UniProtKB:  Q8A9F0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A9F0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
B [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.86α = 90
b = 86.86β = 90
c = 50.992γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing

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  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection