9QBN | pdb_00009qbn

Crystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut3 variant with glycosylation by expression in Pichia pastoris (P_PHL7mut3)

• PDB DOI: https://doi.org/10.2210/pdb9QBN/pdb

• Classification: HYDROLASE
• Organism(s): compost metagenome
• Expression System: Pichia
• Mutation(s): Yes 


• Deposited: 2025-03-03 Released: 2025-09-10 
• Deposition Author(s): Useini, A., Strater, N., Striedner, G., Sonnendecker, C.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Trade-Offs between Stability and Activity of Glycosylated and Non-Glycosylated Polyester Hydrolases PHL7 and PHL7mut3

Fohler, L., Faschingeder, F., Leibetseder, L., Zhao, Z., Useini, A., Strater, N., Sonnendecker, C., Ewing, T.A., Moers, A.P.H.A., Werten, M.W.T., van Vliet, D.M., Julsing, M.K., Zimmermann, W., Striedner, G.

(2025) Acs Es T Eng 

• DOI: https://doi.org/10.1021/acsestengg.5c00272

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.43 kDa 
• Atom Count: 2,587 
• Modeled Residue Count: 264 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant	A	265	compost metagenome	Mutation(s): 4
UniProt
Find proteins for A0AA82WPD4 (unidentified) Explore A0AA82WPD4  Go to UniProtKB:  A0AA82WPD4
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.422	α = 90
b = 63.997	β = 90
c = 101.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
STARANISO	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Useini, A., Strater, N., Striedner, G., Sonnendecker, C.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	887913

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release