3UXV

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.189
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KTK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D]	G [auth B], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
GUN Query on GUN Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C]	H [auth B], J [auth C]	GUANINE C₅ H₅ N₅ O UYTPUPDQBNUYGX-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	F [auth A], I [auth B], M [auth D], N [auth D], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth D]	E [auth A], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M33UXV

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