8JC4 | pdb_00008jc4

Crystal structure of the P450 BM3 heme domain mutant F87A-T268V in complex with Pyd-Pid-Phe and hydroxylamine

PDB DOI: https://doi.org/10.2210/pdb8JC4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-05-10 Released: 2023-12-27
Deposition Author(s): Jiang, Y., Dong, S., Feng, Y., Cong, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.245 (Depositor), 0.240 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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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

C(sp3)-H hydroxylation of Broad-Spectrum Alkanes Catalyzed by an Artificial P450 Peroxygenase Driven by omega-Pyridyl Fatty Acyl Amino Acids.

Qin, X., Jiang, Y., Chen, J., Yao, F., Jin, L., Cong, Z.

(2023) Mol Catal 550

DOI: https://doi.org/10.1016/j.mcat.2023.113618

Macromolecule Content

Total Structure Weight: 109.49 kDa
Atom Count: 7,503
Modeled Residue Count: 895
Deposited Residue Count: 930
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, B	465	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 2 Gene Names: cyp102A1, cyp102, BG04_163 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
UCH (Subject of Investigation/LOI) Query on UCH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B]	E [auth A], G [auth A], K [auth B], M [auth B]	1-pyridin-4-ylpiperidine-4-carboxylic acid C₁₁ H₁₄ N₂ O₂ UISWRUUBFFHGLE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B]
PHE Query on PHE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B]	F [auth A], H [auth A], L [auth B], N [auth B]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth B]
HOA (Subject of Investigation/LOI) Query on HOA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	HYDROXYAMINE H₃ N O AVXURJPOCDRRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]