7TA1 | pdb_00007ta1

Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OAT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.607	α = 90
b = 114.607	β = 90
c = 349.326	γ = 120

Symmetry
Space Group	P 31 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 9M		2021-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.01	99.25	99.8	0.993	6.7	6.1		177531

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.12	99.9		0.417

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OAT	2.2	99.25	23.78	135535	6888	99.79	0.2552	0.2508	0.2508	0.2681	0.2696	39.81

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	13.666
f_angle_d	0.8182
f_chiral_restr	0.0521
f_plane_restr	0.0053
f_bond_d	0.0045

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18951
Nucleic Acid Atoms
Solvent Atoms	896
Heterogen Atoms	118

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
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.