8CI9 | pdb_00008ci9

Deoxypodophyllotoxin Synthase in complex with Tris

• PDB DOI: https://doi.org/10.2210/pdb8CI9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinopodophyllum hexandrum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-09 Released: 2023-06-14 
• Deposition Author(s): Ingold, Z., Lichman, B., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure and mutation of deoxypodophyllotoxin synthase (DPS) from Podophyllum hexandrum

Ingold, Z., Grogan, G., Lichman, B.R.

(2023) Front Catal 3

• DOI: https://doi.org/10.3389/fctls.2023.1178345

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: 35.73 kDa 
• Atom Count: 2,607 
• Modeled Residue Count: 306 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxypodophyllotoxin synthase	A [auth C]	312	Sinopodophyllum hexandrum	Mutation(s): 0  Gene Names: 2-ODD, Phex30848 EC: 1.14.20.8
UniProt
Find proteins for A0A0N9HQ36 (Sinopodophyllum hexandrum) Explore A0A0N9HQ36  Go to UniProtKB:  A0A0N9HQ36

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS (Subject of Investigation/LOI)	C, D [auth C], E [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
FE	B [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.713	α = 90
b = 66.828	β = 105.85
c = 55.209	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Ingold, Z., Lichman, B., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection, Database references