6LL1 | pdb_00006ll1

Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb6LL1/pdb

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

Deposited: 2019-12-21 Released: 2021-01-27
Deposition Author(s): Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.209 (Depositor), 0.214 (DCC)
R-Value Work:
0.153 (Depositor), 0.162 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LL1

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

Literature

Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase

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

To be published.

Macromolecule Content

Total Structure Weight: 137.65 kDa
Atom Count: 9,852
Modeled Residue Count: 1,149
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal oxygenase component of carbazole	A, B, C	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84II6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B]	AA [auth C], D [auth A], Q [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain D [auth A] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain D [auth A] Focus chain Q [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain P [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	HA [auth C], IA [auth C], P [auth A], Y [auth B], Z [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	FA [auth C] GA [auth C] N [auth A] O [auth A] W [auth B] FA [auth C], GA [auth C], N [auth A], O [auth A], W [auth B], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain W [auth B] Focus chain X [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain JA [auth C]	JA [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	EA [auth C] G [auth A] H [auth A] I [auth A] J [auth A] EA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain F [auth A] SDF format, chain S [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B]	CA [auth C], F [auth A], S [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain F [auth A] Focus chain S [auth B] Interactions & Density Focus chain CA [auth C] Focus chain F [auth A] Focus chain S [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain T [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain T [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain T [auth B]	DA [auth C], T [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain T [auth B] Interactions & Density Focus chain DA [auth C] Focus chain T [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain R [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B]	BA [auth C], E [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.209 (Depositor), 0.214 (DCC)
R-Value Work: 0.153 (Depositor), 0.162 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.738	α = 90
b = 91.738	β = 90
c = 240.024	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Suzuki-Minakuchi, C.

Funding Organization	Location	Grant Number
Other private	Japan	--

Revision History (Full details and data files)

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

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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.