6LLM | pdb_00006llm

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

PDB DOI: https://doi.org/10.2210/pdb6LLM/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.210 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (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-2,3-diol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase

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

To be published.

Macromolecule Content

Total Structure Weight: 45.65 kDa
Atom Count: 3,626
Modeled Residue Count: 388
Deposited Residue Count: 392
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	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 5 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 D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BIPHENYL-2,3-DIOL C₁₂ H₁₀ O₂ YKOQAAJBYBTSBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A]	E [auth A], G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]