3UXV | pdb_00003uxv

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ

• PDB DOI: https://doi.org/10.2210/pdb3UXV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-12-05 Released: 2011-12-28 
• Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.189 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ

Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., CSGID

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.51 kDa 
• Atom Count: 10,034 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent 7-cyano-7-deazaguanine reductase	A, B, C, D	290	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: queF, VCM66_0859 EC: 1.7.1.13
UniProt
Find proteins for Q9KTK0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTK0  Go to UniProtKB:  Q9KTK0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth B], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GUN	H [auth B], J [auth C]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
GOL	F [auth A], I [auth B], M [auth D], N [auth D], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], L [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.189 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33uxv

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.368	α = 109.89
b = 71.387	β = 119.61
c = 71.359	γ = 99.46

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary