4J07

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

• PDB DOI: https://doi.org/10.2210/pdb4J07/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium leprae Br4923
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-30 Released: 2013-03-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.246 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Crystal structure of a Probable Riboflavin Synthase, Beta chain RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 93.91 kDa 
• Atom Count: 5,962 
• Modelled Residue Count: 743 
• Deposited Residue Count: 905 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E	181	Mycobacterium leprae Br4923	Mutation(s): 0  Gene Names: MLBr00560, ribH EC: 2.5.1.78
UniProt
Find proteins for B8ZUN3 (Mycobacterium leprae (strain Br4923)) Explore B8ZUN3  Go to UniProtKB:  B8ZUN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], I [auth B], K [auth C], L [auth D], M [auth D], O [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	F [auth A], H [auth B], J [auth C], N [auth D], P [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.246 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 6₅ 2 2
• Diffraction Data: https://doi.org/10.18430/M34J07

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 109.95	β = 90
c = 288.33	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description