7XWW | pdb_00007xww

Crystal structure of NTR in complex with BN-XB

• PDB DOI: https://doi.org/10.2210/pdb7XWW/pdb

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


• Deposited: 2022-05-27 Released: 2023-05-31 
• Deposition Author(s): Chen, X., Chen, J., Li, J.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.379 (Depositor), 0.380 (DCC) 
• R-Value Work: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NTR in complex with BN-XB

Chen, X., Chen, J., Li, J.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.38 kDa 
• Atom Count: 6,850 
• Modeled Residue Count: 864 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteridine reductase	A [auth B], B [auth A], C [auth H], D [auth I]	218	Escherichia coli	Mutation(s): 0  Gene Names: nfnB, nfsB EC: 1.5.1.34 (PDB Primary Data), 1 (UniProt)
UniProt
Find proteins for P38489 (Escherichia coli (strain K12)) Explore P38489  Go to UniProtKB:  P38489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I5O (Subject of Investigation/LOI)	F [auth A]	2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-8-[1-[(4-nitrophenyl)methyl]pyridin-1-ium-4-yl]-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaene C25 H24 B F2 N4 O2 SSXQFDMKTYXSAZ-UHFFFAOYSA-N
FMN (Subject of Investigation/LOI)	E [auth B], G [auth A], H, I	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.379 (Depositor), 0.380 (DCC) 
• R-Value Work:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.87	α = 96.64
b = 61.669	β = 100.83
c = 88.332	γ = 110.72

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Chen, X., Chen, J., Li, J.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21807088

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description