4GHM | pdb_00004ghm

Crystal Structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0

• PDB DOI: https://doi.org/10.2210/pdb4GHM/pdb
• Entry: 4GHM supersedes: 3RZQ

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


• Deposited: 2012-08-08 Released: 2012-09-05 
• 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: 1.62 Å
• R-Value Free: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0

Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (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)

Macromolecule Content 

• Total Structure Weight: 67.16 kDa 
• Atom Count: 4,932 
• Modeled Residue Count: 518 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent 7-cyano-7-deazaguanine reductase	A, B	290	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: queF, VC_0902 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRF	C [auth A], G [auth B]	7-DEAZA-7-AMINOMETHYL-GUANINE C7 H9 N5 O MEYMBLGOKYDGLZ-UHFFFAOYSA-N
GOL	D [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34ghm

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.114	α = 90
b = 72.256	β = 131.26
c = 81.755	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3RZQ

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary