7P6L | pdb_00007p6l

Heme domain of CYP505A30, a fungal hydroxylase from Myceliophthora thermophila, bound to dodecanoic acid

PDB DOI: https://doi.org/10.2210/pdb7P6L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermothelomyces thermophilus ATCC 42464
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-16 Released: 2022-02-09
Deposition Author(s): Opperman, D.J., Aschenbrenner, J.C., Tolmie, C., Ebrecht, A.C.
Funding Organization(s): National Research Foundation in South Africa, Global Challenges Research Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the fungal hydroxylase, CYP505A30, and rational transfer of mutation data from CYP102A1 to alter regioselectivity

Aschenbrenner, J.C., Ebrecht, A.C., Tolmie, C., Smit, M.S., Opperman, D.J.

(2021) Catal Sci Technol 11: 7359-7367

DOI: https://doi.org/10.1039/D1CY01348C

Macromolecule Content

Total Structure Weight: 213.6 kDa
Atom Count: 14,979
Modeled Residue Count: 1,832
Deposited Residue Count: 1,856
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A [auth B], B [auth A], C, D	464	Thermothelomyces thermophilus ATCC 42464	Mutation(s): 0 Gene Names: MYCTH_101224 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for G2QDZ3 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799)) Explore G2QDZ3 Go to UniProtKB: G2QDZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G2QDZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth A] SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	E [auth B], G [auth A], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth B], H [auth A], J [auth C], L [auth D]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.49	α = 90
b = 171.49	β = 90
c = 175.647	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation in South Africa	South Africa	c*change, PAR-02
National Research Foundation in South Africa	South Africa	112094
Global Challenges Research Fund	United Kingdom	ST/R002754/1