2D5N | pdb_00002d5n

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

• PDB DOI: https://doi.org/10.2210/pdb2D5N/pdb

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


• Deposited: 2005-11-02 Released: 2005-11-29 
• Deposition Author(s): Liaw, S.H., Chen, S.J., Chang, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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: 164.05 kDa 
• Atom Count: 11,257 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZN	E [auth A], F [auth B], H [auth C], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.13	α = 90
b = 107.952	β = 90
c = 186.839	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary