Xanthomonas citri Dephospho-PGM in complex with glucose-1,6-bisphosphate

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

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This is version 1.4 of the entry. See complete history


Structural and dynamical description of the enzymatic reaction of a phosphohexomutase.

Stiers, K.M.Graham, A.C.Zhu, J.S.Jakeman, D.L.Nix, J.C.Beamer, L.J.

(2019) Struct Dyn 6: 024703-024703

  • DOI: https://doi.org/10.1063/1.5092803
  • Primary Citation of Related Structures:  
    6NN1, 6NN2, 6NNN, 6NNO, 6NNP, 6NNS, 6NNT, 6NNU, 6NOL, 6NOQ, 6NP8, 6NPX, 6NQE, 6NQF, 6NQG

  • PubMed Abstract: 

    Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri . The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

  • Organizational Affiliation

    Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglucomutase468Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: xanAXAC3579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G16

Download Ideal Coordinates CCD File 
B [auth A]1,6-di-O-phosphono-alpha-D-glucopyranose
C6 H13 O12 P2
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.62α = 90
b = 54.74β = 90
c = 173.29γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1409898

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary