6LLF

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb6LLF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Janthinobacterium sp. J3, Metapseudomonas resinovorans
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.158 (Depositor), 0.170 (DCC)
R-Value Observed:
0.160 (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

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

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

To be published.

Macromolecule Content

Total Structure Weight: 175.59 kDa
Atom Count: 13,321
Modelled Residue Count: 1,479
Deposited Residue Count: 1,521
Unique protein chains: 2

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin CarAc	D, E, F	115	Metapseudomonas resinovorans	Mutation(s): 0 Gene Names: carAc
UniProt
Find proteins for Q8GI16 (Metapseudomonas resinovorans) Explore Q8GI16 Go to UniProtKB: Q8GI16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GI16
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WBP (Subject of Investigation/LOI) Query on WBP Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain U [auth B]	DA [auth C], I [auth A], U [auth B]	3-(2-hydroxyphenyl)benzene-1,2-diol C₁₂ H₁₀ O₃ USBNIYMZDQVDSO-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain I [auth A] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain I [auth A] Focus chain U [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain JA [auth D] SDF format, chain LA [auth E] SDF format, chain NA [auth F] SDF format, chain S [auth B] SDF format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain BA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain BA [auth C]	BA [auth C] G [auth A] JA [auth D] LA [auth E] NA [auth F] BA [auth C], G [auth A], JA [auth D], LA [auth E], NA [auth F], S [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain G [auth A] Focus chain JA [auth D] Focus chain LA [auth E] Focus chain NA [auth F] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain G [auth A] Focus chain JA [auth D] Focus chain LA [auth E] Focus chain NA [auth F] Focus chain S [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain M [auth A] SDF format, chain R [auth A] SDF format, chain X [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] MOL2 format, chain X [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain R [auth A] mmCIF format, chain X [auth B]	IA [auth C], M [auth A], R [auth A], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain M [auth A] Focus chain R [auth A] Focus chain X [auth B] Interactions & Density Focus chain IA [auth C] Focus chain M [auth A] Focus chain R [auth A] Focus chain X [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B]	AA [auth B] EA [auth C] FA [auth C] GA [auth C] HA [auth C] AA [auth B], EA [auth C], FA [auth C], GA [auth C], HA [auth C], J [auth A], K [auth A], KA [auth D], L [auth A], MA [auth E], O [auth A], OA [auth F], P [auth A], Q [auth A], W [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 EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain H [auth A] SDF format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain T [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain T [auth B]	CA [auth C], H [auth A], T [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain H [auth A] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain H [auth A] Focus chain T [auth B]