6LL0 | pdb_00006ll0

Carbazole-soaked reduced oxygenase in carbazole 1,9a-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb6LL0/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: 2.20 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Carbazole-soaked reduced oxygenase in carbazole 1,9a-dioxygenase

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

To be published.

Macromolecule Content

Total Structure Weight: 137.62 kDa
Atom Count: 9,950
Modeled Residue Count: 1,149
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q84II6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain FA [auth C] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain Q [auth B]	D [auth A], FA [auth C], Q [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain FA [auth C] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain FA [auth C] Focus chain Q [auth B]
9CA (Subject of Investigation/LOI) Query on 9CA Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain F [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain F [auth A]	F [auth A], HA [auth C]	9H-CARBAZOLE C₁₂ H₉ N UJOBWOGCFQCDNV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain HA [auth C] Interactions & Density Focus chain F [auth A] Focus chain HA [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	EA [auth B], N [auth A], O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain EA [auth B] Focus chain N [auth A] Focus chain O [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain H [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain U [auth B] SDF format, chain JA [auth C] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain U [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain U [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] G [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], G [auth A], H [auth A], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
FE2 (Subject of Investigation/LOI) Query on FE2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain GA [auth C] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain R [auth B]	E [auth A], GA [auth C], R [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain GA [auth C] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain GA [auth C] Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]