8SBV

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FWM

Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 111.5	β = 90
c = 58.109	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 9M		2022-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9795	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.55	111.5	100	0.057	0.059	0.016	1	21.3	13.2		64479

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59		100	1.565	1.631	0.454	0.664		12.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.55	58.11	1.96	64304	3196	99.8	0.1631	0.162	0.184

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.778
f_angle_d	0.942
f_chiral_restr	0.056
f_bond_d	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3131
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	48

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.