8HIV

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

• PDB DOI: https://doi.org/10.2210/pdb8HIV/pdb

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


• Deposited: 2022-11-22 Released: 2023-07-05 
• 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: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

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

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.49 kDa 
• Atom Count: 2,251 
• Modelled Residue Count: 269 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.677	α = 90
b = 101.677	β = 90
c = 130.922	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Wu, L., Zhou, J.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection