9GWV | pdb_00009gwv

Crystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida in complex with NAD+ (sulfo-ED pathway)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P0DOV5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	. SQDH-NAD complex was achieved using co-crystallization, which was obtained from protein solution at 20 mg/mL in 50 mM TRIS buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop containing 0.1 uL protein: 0.15 uL mother liquor, the latter comprising 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES buffer pH 7.5, 25% v/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
	33.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.893	α = 90
b = 57.021	β = 93.45
c = 91.609	γ = 90

Symmetry
Space Group	I 1 2 1

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 EIGER X 16M		2023-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.9	46.95	99.6	0.095	0.104	0.041	0.995	10.2	6.3		33641

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	1.9	1.94		99.9	0.616	0.676	0.275	0.962		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	46.95	31971	1654	99.48	0.1972	0.1949	0.1949	0.24208	0.2423	RANDOM	33.283

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]
-1.94		2.04	0.81		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.981
r_dihedral_angle_2_deg	10.129
r_dihedral_angle_1_deg	6.596
r_long_range_B_refined	5.884
r_scbond_it	4.076
r_mcangle_it	3.39
r_mcbond_it	2.766
r_angle_refined_deg	2.587
r_chiral_restr	0.181
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3666
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MrBUMP	phasing