3ZI4 | pdb_00003zi4

The structure of Beta-phosphoglucomutase Inhibited With Glucose-6-phosphate and Scandium Tetrafluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 
    0.174 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.130 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.132 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.

Pellegrini, E.Juyoux, P.von Velsen, J.Baxter, N.J.Dannatt, H.R.W.Jin, Y.Cliff, M.J.Waltho, J.P.Bowler, M.W.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.07.007
  • Primary Citation Related Structures: 
    2X13, 2X14, 3ZI4, 4AXX

  • PubMed Abstract: 

    Enzymes facilitating the transfer of phosphate groups constitute the most extensive protein families across all kingdoms of life. They make up approximately 10% of the proteins found in the human genome. Understanding the mechanisms by which enzymes catalyze these reactions is essential in characterizing the processes they regulate. Metal fluorides can be used as multifunctional tools to study these enzymes. These ionic species bear the same charge as phosphate and the transferring phosphoryl group and, in addition, allow the enzyme to be trapped in catalytically important states with spectroscopically sensitive atoms interacting directly with active site residues. The ionic nature of these phosphate surrogates also allows their removal and replacement with other analogs. Here, we describe the best practices to obtain these complexes, their use in NMR, X-ray crystallography, cryo-EM, and SAXS and describe a new metal fluoride, scandium tetrafluoride, which has significant anomalous signal using soft X-rays.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 24.64 kDa 
  • Atom Count: 2,134 
  • Modeled Residue Count: 218 
  • Deposited Residue Count: 221 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-PHOSPHOGLUCOMUTASE221Lactococcus lactisMutation(s): 2 
EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore P71447 
Go to UniProtKB:  P71447
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71447
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free:  0.174 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.130 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.152α = 90
b = 54.238β = 90
c = 104.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Data collection
  • Version 2.0: 2018-02-14
    Changes: Atomic model, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-08-21
    Changes: Database references