2B3Z

Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb2B3Z/pdb

• Classification: HYDROLASE, OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-22 Released: 2005-11-29 
• Deposition Author(s): Chen, S.J., Chang, Y.C., Liaw, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.277 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis

Chen, S.J., Chang, Y.C., Liaw, S.H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 163.3 kDa 
• Atom Count: 11,267 
• Modelled Residue Count: 1,437 
• Deposited Residue Count: 1,492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin biosynthesis protein ribD	A, B, C, D	373	Bacillus subtilis	Mutation(s): 0  Gene Names: RibG EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
UniProt
Find proteins for P17618 (Bacillus subtilis (strain 168)) Explore P17618  Go to UniProtKB:  P17618

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.277 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.322	α = 90
b = 108.45	β = 90
c = 186.977	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): Chen, S.J., Chang, Y.C., Liaw, S.H.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations