9GIZ | pdb_00009giz

UMG-SP-1, a promiscuous hydrolase

• PDB DOI: https://doi.org/10.2210/pdb9GIZ/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-20 Released: 2025-09-03 
• Deposition Author(s): Tokoli, A., Stojanovski, G., Jodaitis, L., Hollfelder, F., Hyvonen, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: in silico

Literature

Structure of UMG-SP-1 at 1.89 Angstroms resolution

Tokoli, A., Stjoanovski, G., Jodaitis, L., Hollfelder, F., Hyvonen, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.2 kDa 
• Atom Count: 6,045 
• Modeled Residue Count: 779 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UMG-SP-1	A, B	438	uncultured bacterium	Mutation(s): 0  EC: 3.5.1.75 (PDB Primary Data), 3.5.1.4 (UniProt)
UniProt
Find proteins for A0A7W9ANY4 (Sphingomonas yantingensis) Explore A0A7W9ANY4  Go to UniProtKB:  A0A7W9ANY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.873	α = 90
b = 108.335	β = 90
c = 114.218	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Tokoli, A., Stojanovski, G., Jodaitis, L., Hollfelder, F., Hyvonen, M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X00306X/1

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release