8XBQ | pdb_00008xbq

Crystal structure of activity improved formolase variant K1

• PDB DOI: https://doi.org/10.2210/pdb8XBQ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-12-06 Released: 2024-12-11 
• Deposition Author(s): Wei, H.L., Cheng, Y.Y., Tang, Z.J., Tan, Z.J., Liu, W.D., Zhu, L.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Helix Zipper Regulating Formolase Activity.

Tan, Z.J., Tang, Z.J., Wei, H.L., Zhang, R., Sun, L., Liu, W.D., Liu, H.F., Zhu, L.L., Ma, Y.H.

(2025) ACS Catal 15: 1586-1595

• DOI: https://doi.org/10.1021/acscatal.4c07452

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

Macromolecule Content 

• Total Structure Weight: 56.89 kDa 
• Atom Count: 4,326 
• Modeled Residue Count: 524 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase-K2	A	528	Pseudomonas putida	Mutation(s): 8  Gene Names: mdlC EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida) Explore P20906  Go to UniProtKB:  P20906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	B [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.271	α = 90
b = 99.376	β = 90
c = 110.092	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wei, H.L., Cheng, Y.Y., Tang, Z.J., Tan, Z.J., Liu, W.D., Zhu, L.L.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Database references, Structure summary