8WMY | pdb_00008wmy

Crystal structure of YqeK in complex with MG and ADP.

  • Classification: HYDROLASE
  • Organism(s): Staphylococcus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-10-05 Released: 2023-10-25 
  • Deposition Author(s): Mo, X.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Molecular Mechanism of Ap4A Hydrolysis by YqeK of Staphylococcus pyogenes.

Mo, X.

To be published.

Macromolecule Content 

  • Total Structure Weight: 45.93 kDa 
  • Atom Count: 3,494 
  • Modeled Residue Count: 392 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
A, B
198StaphylococcusMutation(s): 0 
Gene Names: E0F66_02650, SAMEA1711581_00596, SAMEA864267_01112
EC: 3.6.1.41
UniProt
Find proteins for A0A4U7IGH6 (Streptococcus pyogenes)
Explore A0A4U7IGH6 
Go to UniProtKB:  A0A4U7IGH6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4U7IGH6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.944α = 90
b = 37.672β = 92.704
c = 76.301γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-10-25 
    • Deposition Author(s): Mo, X.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071476

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Advisory, Derived calculations, Structure summary