6LLK

Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase

• PDB DOI: https://doi.org/10.2210/pdb6LLK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Janthinobacterium sp. J3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-23 Released: 2021-01-27 
• Deposition Author(s): Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase

Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.54 kDa 
• Atom Count: 3,437 
• Modelled Residue Count: 386 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal oxygenase component of carbazole	A	392	Janthinobacterium sp. J3	Mutation(s): 0  Gene Names: carAa
UniProt
Find proteins for Q84II6 (Janthinobacterium sp. (strain J3)) Explore Q84II6  Go to UniProtKB:  Q84II6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WBP (Subject of Investigation/LOI)	D [auth A]	3-(2-hydroxyphenyl)benzene-1,2-diol C12 H10 O3 USBNIYMZDQVDSO-UHFFFAOYSA-N
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MPD	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.361	α = 90
b = 131.361	β = 90
c = 131.361	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.

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Funding Organization	Location	Grant Number
Other private	Japan	--

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description