1RLJ | pdb_00001rlj

Structural Genomics, a Flavoprotein NrdI from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1RLJ/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-11-25 Released: 2004-07-13 
• Deposition Author(s): Wu, R., Zhang, R., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

1.5A crystal structure of a thioredoxin-like protein NrdI from Bacillus subtilis

Wu, R., Zhang, R., Collart, F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.4 kDa 
• Atom Count: 1,239 
• Modeled Residue Count: 135 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrdI protein	A	139	Bacillus subtilis	Mutation(s): 0  Gene Names: NRDI, BSU17370
UniProt
Find proteins for P50618 (Bacillus subtilis (strain 168)) Explore P50618  Go to UniProtKB:  P50618

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
IOD	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.236	α = 90
b = 85.236	β = 90
c = 59.992	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-13 
Deposition Author(s): Wu, R., Zhang, R., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations