9HDE | pdb_00009hde

Crystal structure of methionine gamma-lyase (K209Q variant) from Brevibacterium aurantiacum in complex with PLP and alpha-ketobutyrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GJ9	Methionine gamma-lyase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	Well solution 0.1 M Tris-HCl, pH 8.5, 0.1 M Lithium sulfate, 32% PEG4000, 1 mM PLP, 20 mM Methionine, Cryoprotection: 10% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.48	47.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.328	α = 90
b = 155.89	β = 90.24
c = 232.079	γ = 90

Symmetry
Space Group	P 1 21 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	a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors	2023-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98399	SOLEIL	PROXIMA 2

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	2.522	232.077	93.6	0.3218	0.3498	0.1356	0.98	5.9	6.32		214191

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)
	2.522	2.82	61.6		1.2192	1.3263	0.5162	0.44	1.63	6.27	10710

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	2.522	232.08	214191	10624	67.2	0.2581	0.2577	0.2474	0.2652	0.2558	RANDOM	59.77

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]
1.2175		2.9363	-3.5211		2.3036

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.47
t_omega_torsion	2.39
t_angle_deg	0.96
t_bond_d	0.008
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	67475
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	652

Software

Software
Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
Coot	model building
BUSTER	refinement
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.