7X2Q | pdb_00007x2q

Salvia miltiorrhiza CYP76AH3

PDB DOI: https://doi.org/10.2210/pdb7X2Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salvia miltiorrhiza
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2022-02-26 Released: 2023-03-01
Deposition Author(s): Chang, Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.68 Å
R-Value Free:
0.296 (Depositor), 0.290 (DCC)
R-Value Work:
0.251 (Depositor), 0.250 (DCC)
R-Value Observed:
0.254 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of CYP76AH3 at 3.67 Angstroms resolution

Chang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 108.55 kDa
Atom Count: 7,506
Modeled Residue Count: 934
Deposited Residue Count: 952
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugiol synthase	A, B	476	Salvia miltiorrhiza	Mutation(s): 0 Gene Names: CYP76AH3 EC: 1.14.14.65 (PDB Primary Data), 1.14.14.60 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for A0A0Y0GRS3 (Salvia miltiorrhiza) Explore A0A0Y0GRS3 Go to UniProtKB: A0A0Y0GRS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0Y0GRS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.68 Å
R-Value Free: 0.296 (Depositor), 0.290 (DCC)
R-Value Work: 0.251 (Depositor), 0.250 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.1	α = 90
b = 151.1	β = 90
c = 156.91	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-03-01
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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.