9KW7 | pdb_00009kw7

Polyether epoxide hydrolase MonBI K7A mutant

• PDB DOI: https://doi.org/10.2210/pdb9KW7/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces virginiae
• Expression System: Escherichia
• Mutation(s): Yes 


• Deposited: 2024-12-05 Released: 2025-12-10 
• Deposition Author(s): Yao, M., Arai, A., Minami, A., Ozaki, T., Kumeta, H., Oikawa, H., Ose, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

A paring system of polyether epoxide hydrolases enables a mouldable enzyme for consecutive ring cyclisation cascade

Yabuno, N., Minami, A., Ozaki, T., Owada, Y., Sawada, K., Arai, A., Tadokoro, T., Aizawa, T., Dosen, T., Nomai, T., Matsumaru, T., Junyang, L., Tao, Y., Kodama, A., Uchiyama, S., Hengphasatporn, K., Shigeta, Y., Saio, T., Maenaka, K., Yao, M., Kumeta, H., Oikawa, H., Ose, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.05 kDa 
• Atom Count: 2,278 
• Modeled Residue Count: 284 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MonBI	A [auth B], B [auth A]	160	Streptomyces virginiae	Mutation(s): 1  Gene Names: monBI
UniProt
Find proteins for Q846W7 (Streptomyces virginiae) Explore Q846W7  Go to UniProtKB:  Q846W7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth B], D [auth B], E [auth B], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.981	α = 90
b = 135.981	β = 90
c = 66.175	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Yao, M., Arai, A., Minami, A., Ozaki, T., Kumeta, H., Oikawa, H., Ose, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H04634
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H01754
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22K19282

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release