5YLW | pdb_00005ylw

CYP76AH1 from Salvia miltiorrhiza

• PDB DOI: https://doi.org/10.2210/pdb5YLW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salvia miltiorrhiza
• Expression System: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2017-10-20 Released: 2018-10-24 
• Deposition Author(s): Chang, Z.
• Funding Organization(s): The National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

CYP76AH1 from Salvia miltiorrhiza

Chang, Z.

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

Macromolecule Content

• Total Structure Weight: 56.26 kDa 
• Atom Count: 4,321 
• Modelled Residue Count: 466 
• Deposited Residue Count: 495 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferruginol synthase	A	495	Salvia miltiorrhiza	Mutation(s): 0  Gene Names: CYP76AH1 EC: 1.14.13.190 (PDB Primary Data), 1.14.14.175 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for S4UX02 (Salvia miltiorrhiza) Explore S4UX02  Go to UniProtKB:  S4UX02

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.776	α = 90
b = 108.776	β = 90
c = 105.99	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MoRDa	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Chang, Z.

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Funding Organization	Location	Grant Number
The National Natural Science Foundation of China	China	81773833

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations, Refinement description