3UXJ

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0

PDB DOI: https://doi.org/10.2210/pdb3UXJ/pdb

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

Deposited: 2011-12-05 Released: 2012-01-04
Deposition Author(s): Kim, Y., Zhang, R., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.165 (Depositor), 0.160 (DCC)
R-Value Work:
0.132 (Depositor), 0.120 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0

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

To be published.

Macromolecule Content

Total Structure Weight: 135.85 kDa
Atom Count: 10,263
Modelled Residue Count: 1,040
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 LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain R [auth D]	F [auth A], R [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain R [auth D]
PRF Query on PRF Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C]	E [auth A], I [auth B], O [auth C], S [auth D]	7-DEAZA-7-AMINOMETHYL-GUANINE C₇ H₉ N₅ O MEYMBLGOKYDGLZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain S [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	G [auth A] H [auth A] J [auth B] K [auth B] L [auth B] G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C]

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: 1.40 Å
R-Value Free: 0.165 (Depositor), 0.160 (DCC)
R-Value Work: 0.132 (Depositor), 0.120 (DCC)
R-Value Observed: 0.134 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33uxj

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.387	α = 110.01
b = 71.416	β = 119.54
c = 71.358	γ = 99.46

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-01-04
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: 2024-10-16
Changes: Structure summary