6JZM | pdb_00006jzm

The intermediate forming O-C10 bond formation in AsqJ-catalyzed epoxidation

PDB DOI: https://doi.org/10.2210/pdb6JZM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus nidulans FGSC A4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-02 Released: 2020-03-18
Deposition Author(s): Liao, H.J., Chan, N.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.214 (Depositor), 0.209 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

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Literature

The intermediate forming O-C10 bond formation in AsqJ-catalyzed epoxidation

Liao, H.J., Chan, N.L.

(2020) J Am Chem Soc

Macromolecule Content

Total Structure Weight: 34.49 kDa
Atom Count: 2,478
Modeled Residue Count: 287
Deposited Residue Count: 308
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron/alpha-ketoglutarate-dependent dioxygenase asqJ	A [auth B]	308	Aspergillus nidulans FGSC A4	Mutation(s): 0 Gene Names: asqJ, AN9227 EC: 1.14 (PDB Primary Data), 1.14.11.81 (UniProt)
UniProt
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q5AR53 Go to UniProtKB: Q5AR53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5AR53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CQ9 (Subject of Investigation/LOI) Query on CQ9 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(3~{R},3'~{S})-4-methyl-3'-phenyl-spiro[1~{H}-1,4-benzodiazepine-3,2'-oxirane]-2,5-dione C₁₇ H₁₄ N₂ O₃ APLKWZASYUZSBL-WMLDXEAASA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.214 (Depositor), 0.209 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.147	α = 90
b = 121.805	β = 90
c = 66.617	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.