8W7G

Crystal structure of cytochrome P450 CYP161H12 from Amycolatopsis pretoriensis

PDB DOI: https://doi.org/10.2210/pdb8W7G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amycolatopsis pretoriensis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-08-30 Released: 2024-09-04
Deposition Author(s): Dong, L.B., Zhang, X.W., Pan, X.M., Li, F.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Explore the chemical space of Pentacyclic Triterpenoids: Mining Bacterial CYP450s for Aliphatic C-H Activation

Zhang, X.W., Dong, L.B.

To be published.

Macromolecule Content

Total Structure Weight: 46.39 kDa
Atom Count: 3,440
Modelled Residue Count: 390
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentalenolactone synthase	A	416	Amycolatopsis pretoriensis	Mutation(s): 0 Gene Names: SAMN05421837_113114
UniProt
Find proteins for A0A1H5RFX8 (Amycolatopsis pretoriensis) Explore A0A1H5RFX8 Go to UniProtKB: A0A1H5RFX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H5RFX8
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: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.78	α = 90
b = 75.78	β = 90
c = 141.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82073746

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release

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.