8SBV

Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (ADP bound)

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	2022-02-14
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 2
Unit cell lengths	67.520, 111.500, 58.109
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	58.110 - 1.550
R-factor	0.1631
Rwork	0.162
R-free	0.18400
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.942
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.21rc1_4918: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	111.500	1.590
High resolution limit [Å]	1.550	1.550
Rmerge	0.057	1.565
Rmeas	0.059	1.631
Rpim	0.016	0.454
Total number of observations	850931	60272
Number of reflections	64479	4730
<I/σ(I)>	21.3	1.8
Completeness [%]	100.0
Redundancy	13.2	12.7
CC(1/2)	1.000	0.664

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4.4	291	0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0603, Cryo: 2.5 M lithium sulfate. 2mM NAD added prior to crystallization. However, ADP modeled in replace of NAD, as NAD appears to have been hydrolysed at acidic pH (4.4). The nicotimide side clearly not visible. One subunit of the protein binds ADP