5W4Z | pdb_00005w4z

Crystal Structure of Riboflavin Lyase (RcaE) with modified FMN and substrate Riboflavin

• PDB DOI: https://doi.org/10.2210/pdb5W4Z/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Herbiconiux
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-13 Released: 2018-06-13 
• Deposition Author(s): Bhandari, D.M., Chakrabarty, Y., Zhao, B., Wood, J., Li, P., Begley, T.P.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Cannibalism Among the Flavins: a Novel C-N Bond Cleavage in Riboflavin Catabolism Mediated by Flavin-Generated Superoxide Radical

Chakrabarty, Y., Bhandari, D.M., Zhao, B., Wood, J., Li, P., Begley, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 102.19 kDa 
• Atom Count: 7,437 
• Modeled Residue Count: 893 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin Lyase	A, B	461	Herbiconiux	Mutation(s): 0  Gene Names: RcaE
UniProt
Find proteins for A0A3B6UEK8 (Herbiconiux) Explore A0A3B6UEK8  Go to UniProtKB:  A0A3B6UEK8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9WY	C [auth A], E [auth B]	1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-3-O-phosphono-D-ribitol C17 H21 N4 O9 P XTUPYSORVVXTTQ-AOUZGSJDSA-N
RBF	D [auth A], F [auth B]	RIBOFLAVIN C17 H20 N4 O6 AUNGANRZJHBGPY-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.97	α = 90
b = 108.8	β = 90
c = 125.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
PHENIX	model building
iMOSFLM	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Bhandari, D.M., Chakrabarty, Y., Zhao, B., Wood, J., Li, P., Begley, T.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK44083
Robert A. Welch Foundation	United States	A-0034

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description