8X1W | pdb_00008x1w

CYP725A4 apo structure

PDB DOI: https://doi.org/10.2210/pdb8X1W/pdb

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

Deposited: 2023-11-09 Released: 2024-08-14
Deposition Author(s): Chang, Z., Wang, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.238 (Depositor), 0.237 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

Total Structure Weight: 50.75 kDa
Atom Count: 3,668
Modeled Residue Count: 439
Deposited Residue Count: 439
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Taxadiene 5-alpha hydroxylase	A	439	Taxus cuspidata	Mutation(s): 0 EC: 1.14.14.176
UniProt
Find proteins for Q6WG30 (Taxus cuspidata) Explore Q6WG30 Go to UniProtKB: Q6WG30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6WG30
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.238 (Depositor), 0.237 (DCC)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.02	α = 90
b = 196.02	β = 90
c = 196.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release
Version 1.1: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.