7CB9 | pdb_00007cb9

CYP76AH1/miltiradiene from Salvia miltiorrhiza

PDB DOI: https://doi.org/10.2210/pdb7CB9/pdb

Classification: PLANT PROTEIN
Organism(s): Salvia miltiorrhiza
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-11 Released: 2021-06-16
Deposition Author(s): Chang, Z., Chao, S., Mingyue, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.229 (Depositor), 0.226 (DCC)
R-Value Work:
0.220 (Depositor), 0.218 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CYP76AH1 from Salvia miltiorrhiza

Chang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 56.48 kDa
Atom Count: 4,246
Modeled Residue Count: 466
Deposited Residue Count: 495
Unique protein chains: 1

Macromolecules

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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)
UniProt
Find proteins for S4UX02 (Salvia miltiorrhiza) Explore S4UX02 Go to UniProtKB: S4UX02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S4UX02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
J6C (Subject of Investigation/LOI) Query on J6C Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Miltiradiene C₂₀ H₃₂ BGVUIJDZTQIJIO-AZUAARDMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229 (Depositor), 0.226 (DCC)
R-Value Work: 0.220 (Depositor), 0.218 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.5	α = 90
b = 108.5	β = 90
c = 105.685	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81773833

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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.