6LLH | pdb_00006llh

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

PDB DOI: https://doi.org/10.2210/pdb6LLH/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: 1.99 Å
R-Value Free:
0.207 (Depositor), 0.202 (DCC)
R-Value Work:
0.162 (Depositor)
R-Value Observed:
0.164 (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: 175.25 kDa
Atom Count: 13,006
Modeled Residue Count: 1,480
Deposited Residue Count: 1,521
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84II6
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GI16
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BPY (Subject of Investigation/LOI) Query on BPY Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth C]	I [auth A], Q [auth B], Z [auth C]	BIPHENYL-2,3-DIOL C₁₂ H₁₀ O₂ YKOQAAJBYBTSBS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B] Focus chain Z [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain IA [auth F] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C]	EA [auth D] FA [auth E] H [auth A] IA [auth F] P [auth B] EA [auth D], FA [auth E], H [auth A], IA [auth F], P [auth B], Y [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth E] Focus chain H [auth A] Focus chain IA [auth F] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth E] Focus chain H [auth A] Focus chain IA [auth F] Focus chain P [auth B] Focus chain Y [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain K [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A]	HA [auth E], K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain K [auth A] Interactions & Density Focus chain HA [auth E] Focus chain K [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain GA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] mmCIF format, chain GA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B]	GA [auth E], M [auth A], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain GA [auth E] Focus chain M [auth A] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain BA [auth C]	BA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B]	AA [auth C] CA [auth C] DA [auth C] J [auth A] N [auth A] AA [auth C], CA [auth C], DA [auth C], J [auth A], N [auth A], R [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain J [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain J [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain X [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C] mmCIF format, chain G [auth A]	G [auth A], O [auth B], X [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain X [auth C]