7V3O | pdb_00007v3o

The structure of Se-SoBcmB with Fe(II)and AKG

• PDB DOI: https://doi.org/10.2210/pdb7V3O/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.75 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 277 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe/2OG dependent dioxygenase	A	328	Streptomyces ossamyceticus	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YA87 (Streptomyces ossamyceticus) Explore A0A9Y2YA87  Go to UniProtKB:  A0A9Y2YA87

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	B [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.62	α = 90
b = 101.62	β = 90
c = 130.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Wu, L., Zhou, J.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Data collection, Database references
• Version 1.2: 2024-11-06
  Changes: Structure summary