7V2X

The complex structure of soBcmB and its substrate 1

• PDB DOI: https://doi.org/10.2210/pdb7V2X/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: 2.08 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

The crystal structure of SoBcmB and its side way substrate

Wu, L., Zhou, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.84 kDa 
• Atom Count: 2,359 
• Modelled Residue Count: 280 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dioxygenase	A	328	Streptomyces ossamyceticus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7QX (Subject of Investigation/LOI)	E [auth A]	(3S,6S)-3-[(2S)-butan-2-yl]-6-[(2R)-2-methyl-2,3-bis(oxidanyl)propyl]piperazine-2,5-dion C12 H22 N2 O4 KJJLKZILTAEYLN-PHGLEFOZSA-N
AKG (Subject of Investigation/LOI)	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.097	α = 90
b = 101.097	β = 90
c = 130.377	γ = 120

Software Package:

Software Name	Purpose
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: 2023-11-29
  Changes: Data collection, Refinement description