2X2O

The flavoprotein NrdI from Bacillus cereus with the initially oxidized FMN cofactor in an intermediate radiation reduced state

• PDB DOI: https://doi.org/10.2210/pdb2X2O/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-15 Released: 2010-03-09 
• Deposition Author(s): Rohr, A.K., Hersleth, H.P., Andersson, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.173 

Starting Model: experimental

Literature

Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and Qm/Mm Calculations

Rohr, A.K., Hersleth, H.P., Andersson, K.K.

(2010) Angew Chem Int Ed Engl 49: 2324

• PubMed: 20187055 
• DOI: https://doi.org/10.1002/anie.200907143
• Primary Citation of Related Structures:  
  2X2O, 2X2P

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Organizational Affiliation: 

Department of Molecular Biosciences, University of Oslo, 0316 Oslo, Norway.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 14.39 kDa 
• Atom Count: 1,185 
• Modelled Residue Count: 117 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRDI PROTEIN	A	119	Bacillus cereus ATCC 14579	Mutation(s): 0
UniProt
Find proteins for Q81G57 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81G57  Go to UniProtKB:  Q81G57

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CAC	G [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.855	α = 90
b = 45.765	β = 90
c = 56.745	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Rohr, A.K., Hersleth, H.P., Andersson, K.K.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Database references, Derived calculations, Non-polymer description, Version format compliance
• Version 1.2: 2019-05-22
  Changes: Data collection, Other, Refinement description
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description