9YFK

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-06-07
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	I 1 2 1
Unit cell lengths	93.397, 71.027, 93.487
Unit cell angles	90.00, 90.06, 90.00

Refinement procedure

Resolution	46.740 - 1.680
R-factor	0.1777
Rwork	0.168
R-free	0.20450
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	0.957
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5819: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.740	1.720
High resolution limit [Å]	1.680	1.680
Rmerge	0.083	1.091
Rmeas	0.090	1.180
Rpim	0.035	0.444
Total number of observations	470183	35898
Number of reflections	69602	5172
<I/σ(I)>	12.2	1.6
Completeness [%]	99.8
Redundancy	6.8	6.9
CC(1/2)	0.997	0.553

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Berkeley B1: 30% PEG 3350, 400 mM NaCl, 100 mM Tris, pH 8.5. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM UTP, 2mM D-glucose-1-phosphate and 2mM MgCl2 added to protein prior to crystallization. The product URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG) was bound. plate 19925 B1 drop 3, Puck: PSL-0713, Cryo: 80% crystallant + 20% glycerol