9O8Y

Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound)

This is a non-PDB format compatible entry.

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	2025-03-15
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	86.264, 88.645, 117.291
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.910 - 1.450
R-factor	0.1605
Rwork	0.159
R-free	0.18240
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	0.961
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (dev_5660)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.910	1.470
High resolution limit [Å]	1.450	1.450
Rmerge	0.083	1.735
Rmeas	0.086	1.800
Rpim	0.023	0.476
Total number of observations	2145348	109008
Number of reflections	159318	7804
<I/σ(I)>	17.2	1.6
Completeness [%]	100.0
Redundancy	13.5	14
CC(1/2)	1.000	0.415

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5	291	Proplex B8: 15% w/v PEG 4000, 0.1 M sodium citrate pH 5.0, 0.1 M magnesium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. 2mM succinyl-CoA added prior to crystallization. Bound in one subunit only. plate 19707 A1 drop 1, Puck: PSL1209, Cryo: 80% crystallant + 20% PEG 200.