3BL5 | pdb_00003bl5

Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis

PDB DOI: https://doi.org/10.2210/pdb3BL5/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-10 Released: 2008-06-03
Deposition Author(s): Cicmil, N., Huang, R.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.222 (Depositor), 0.228 (DCC)
R-Value Observed:
0.249 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of QueC from Bacillus subtilis: An enzyme involved in preQ(1) biosynthesis.

Cicmil, N., Huang, R.H.

(2008) Proteins 72: 1084-1088

PubMed: 18491386 Search on PubMed
DOI: https://doi.org/10.1002/prot.22098
Primary Citation Related Structures:
3BL5

Organizational Affiliation

Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Macromolecule Content

Total Structure Weight: 148.45 kDa
Atom Count: 9,341
Modeled Residue Count: 1,178
Deposited Residue Count: 1,314
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuosine biosynthesis protein queC	A, B, C, D, E A, B, C, D, E, F	219	Bacillus subtilis	Mutation(s): 0 Gene Names: queC, ykvJ EC: 3.5 (PDB Primary Data), 6.3.4.20 (UniProt)
UniProt
Find proteins for O31675 (Bacillus subtilis (strain 168)) Explore O31675 Go to UniProtKB: O31675
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31675
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain H [auth A]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.272 (Depositor), 0.273 (DCC)
R-Value Work: 0.222 (Depositor), 0.228 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.057	α = 90
b = 75.542	β = 94.73
c = 131.023	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Cicmil, N.

Huang, R.H.

Revision History (Full details and data files)

Version 1.0: 2008-06-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations