8JRL | pdb_00008jrl

Crystal structure of P450 TleB with an indole alkaloid

PDB DOI: https://doi.org/10.2210/pdb8JRL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces blastmyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-17 Released: 2024-04-17
Deposition Author(s): Wang, J., Yan, W.P.
Funding Organization(s): Science and Technology Commission of Shanghai

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.208 (Depositor), 0.211 (DCC)
R-Value Work:
0.167 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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Literature

Regulation of P450 TleB catalytic flow for the synthesis of sulfur-containing indole alkaloids by substrate structure-directed strategy. and protein engineering.

Ge, X.Y., Long, Y., Wang, J., Gu, B., Yang, Z.X., Feng, Y.Y., Zheng, S., Li, Y.Y., Yan, W.P., Song, H.

(2023) Sci China B Chem 66: 3232-3241

DOI: https://doi.org/10.1007/s11426-023-1755-4

Macromolecule Content

Total Structure Weight: 47.96 kDa
Atom Count: 3,410
Modeled Residue Count: 392
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450	A	418	Streptomyces blastmyceticus	Mutation(s): 0 Gene Names: tleB
UniProt
Find proteins for A0A077KEB8 (Streptomyces blastmyceticus) Explore A0A077KEB8 Go to UniProtKB: A0A077KEB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077KEB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
V3X (Subject of Investigation/LOI) Query on V3X Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2~{S})-~{N}-[(2~{S})-1-(4-fluoranyl-1~{H}-indol-3-yl)-3-oxidanyl-propan-2-yl]-3-methyl-2-sulfanyl-butanamide C₁₆ H₂₁ F N₂ O₂ S KKPTZRIROSBPNX-NHYWBVRUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.208 (Depositor), 0.211 (DCC)
R-Value Work: 0.167 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.035	α = 90
b = 85.587	β = 90
c = 113.755	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Technology Commission of Shanghai	China	21ZR1433700

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.