8P37 | pdb_00008p37

Structure a catalytically inactive mutant of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	SynGUAB3-C222S crystals were grown in the presence of IMP and NAD+ in mother liquor from the condition 2-48 of the commercial screen Morpheus (Molecular Dimensions), which consists of an amino acid mixture (0.02M DL-Glutamic acid monohydrate, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine monohydrochloride, and 0.02M DL-Serine, a precipitant mix (25% (v/v) PEG 500 MME and 12.5 % (w/v) PEG 20000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5. Initial conditions: Buffer: 10 mM TrisHCl, pH 8.0 Protein concentration = 15 mg/mL Substrate concentration: 3 mM NAD + 3 mM IMP

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.867	α = 90
b = 112.867	β = 90
c = 54.119	γ = 90

Symmetry
Space Group	I 4

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 PILATUS 6M		2022-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979181423454	ALBA	XALOC

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	1.219	39.905	94	0.0877	0.0914	0.0254	0.999	14.54	12.82		77746

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)
	1.219	1.284	80.1		1.558	1.6279	0.4665	0.68	1.51	11.92	3886

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	1.219	39.91	77746	3882	76.7	0.1755	0.1749	0.18	0.1876	0.19	RANDOM	16.64

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]
0.2698			0.2698		-0.5396

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.46
t_omega_torsion	4.9
t_angle_deg	1.29
t_bond_d	0.013
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2753
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	68

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
autoPROC	data processing
Aimless	data scaling
autoPROC	data processing
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.