7V3E | pdb_00007v3e

The complex structure of soBcmB and its intermediate product 1a

PDB DOI: https://doi.org/10.2210/pdb7V3E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces ossamyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-10 Released: 2023-02-15
Deposition Author(s): Wu, L., Zhou, J.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

He, J.B., Wu, L., Wei, W., Meng, S., Liu, Z.T., Wu, X., Pan, H.X., Yang, S., Liang, Y., Zhou, J., Tang, G.L.

(2023) Nat Catal 6: 637-648

DOI: https://doi.org/10.1038/s41929-023-00987-4

Macromolecule Content

Total Structure Weight: 113.38 kDa
Atom Count: 7,013
Modeled Residue Count: 840
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dioxygenase	A, B, C	328	Streptomyces ossamyceticus	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YA87 (Streptomyces ossamyceticus) Explore A0A9Y2YA87 Go to UniProtKB: A0A9Y2YA87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9Y2YA87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5WI Query on 5WI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain L [auth C]	E [auth A], G [auth B], L [auth C]	(3S,6Z)-3-[(2S)-butan-2-yl]-6-[(2R)-2-methyl-2,3-bis(oxidanyl)propylidene]piperazine-2,5-dione C₁₂ H₂₀ N₂ O₄ KGPSCQPJVWXIGR-PMSMWWAASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C]
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C]	D [auth A], H [auth B], M [auth C]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	F [auth A], I [auth B], N [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]