5JTD

Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L407C heme domain mutant in complex with DMSO.

PDB DOI: https://doi.org/10.2210/pdb5JTD/pdb

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

Deposited: 2016-05-09 Released: 2016-10-12
Deposition Author(s): Kloos, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Insights into an efficient light-driven hybrid P450 BM3 enzyme from crystallographic, spectroscopic and biochemical studies.

Spradlin, J., Lee, D., Mahadevan, S., Mahomed, M., Tang, L., Lam, Q., Colbert, A., Shafaat, O.S., Goodin, D., Kloos, M., Kato, M., Cheruzel, L.E.

(2016) Biochim Biophys Acta 1864: 1732-1738

PubMed: 27639964 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bbapap.2016.09.005
Primary Citation of Related Structures:
5JQ2, 5JTD

PubMed Abstract:
In order to perform selective CH functionalization upon visible light irradiation, Ru(II)-diimine functionalized P450 heme enzymes have been developed. The sL407C-1 enzyme containing the Ru(bpy) ₂PhenA (bpy=2,2'-bipyridine and PhenA=5-acetamido-1,10-phenanthroline) photosensitizer (1) covalently attached to the non-native single cysteine L407C of the P450BM3 heme domain mutant, displays high photocatalytic activity in the selective CH bond hydroxylation of several substrates.

Organizational Affiliation

San José State University, Department of Chemistry, One Washington Square, San José, CA, United States.

Macromolecule Content

Total Structure Weight: 110.47 kDa
Atom Count: 8,328
Modelled Residue Count: 916
Deposited Residue Count: 938
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	469	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 1 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU8 Query on RU8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[2-iodo-N-(1,10-phenanthrolin-5-yl-kappa~2~N~1~,N~10~)acetamide]ruthenium(2+) C₃₄ H₂₆ I N₇ O Ru IMVNBPJSKRZLRT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B]	D [auth A], F [auth A], H [auth B], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.69	α = 90
b = 145.39	β = 97.08
c = 62.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Kloos, M.

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description