8X3E | pdb_00008x3e

CYP725A4-Taxa-4,11-diene complex

• PDB DOI: https://doi.org/10.2210/pdb8X3E/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Taxus cuspidata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-13 Released: 2024-08-14 
• Deposition Author(s): Chang, Z., Wang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.300 (DCC) 

Starting Model: experimental

Literature

Unraveling the Catalytic Mechanism of Taxadiene-5alpha-hydroxylase from Crystallography and Computational Analyses.

Song, X., Wang, Q., Zhu, X., Fang, W., Liu, X., Shi, C., Chang, Z., Jiang, H., Wang, B.

(2024) ACS Catal 14: 3912-3925

• DOI: https://doi.org/10.1021/acscatal.3c05807

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 49.28 kDa 
• Atom Count: 3,548 
• Modeled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Taxadiene 5-alpha hydroxylase	A	424	Taxus cuspidata	Mutation(s): 0  EC: 1.14.14.176
UniProt
Find proteins for Q6WG30 (Taxus cuspidata) Explore Q6WG30  Go to UniProtKB:  Q6WG30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1L3H (Subject of Investigation/LOI)	B [auth A]	(1~{R},3~{R},8~{R})-4,8,12,15,15-pentamethyltricyclo[9.3.1.0^{3,8}]pentadeca-4,11-diene C20 H32 FRJSECSOXKQMOD-IMFGXOCKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.300 (DCC) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.824	α = 90
b = 196.824	β = 90
c = 196.824	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Chang, Z., Wang, Q.

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

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release