5YNL | pdb_00005ynl

Structure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.1M sodium malonate pH 5, 12 % w/v polyethylene glycol 3,350, 0.1 M TCEP hydrochloride, 10mg/ml purified protein

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.193	α = 90
b = 91.193	β = 90
c = 107.779	γ = 120

Symmetry
Space Group	H 3

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 200K		2016-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.54178

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	2.349	63.7	95	0.772	1.6	3.7		13850

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	2.35	2.53			0.772

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 (All)	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	2.35	28.784	13781	689	98.994	0.223	0.2206	0.2206	0.2798	0.28	RANDOM	57.643

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]
0.876	0.438		0.876		-2.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.308
r_dihedral_angle_6_deg	14.47
r_dihedral_angle_2_deg	10.106
r_dihedral_angle_1_deg	9.494
r_lrange_it	7.412
r_scangle_it	4.307
r_mcangle_it	4.3
r_scbond_it	2.981
r_mcbond_it	2.8
r_angle_refined_deg	2.285

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.308
r_dihedral_angle_6_deg	14.47
r_dihedral_angle_2_deg	10.106
r_dihedral_angle_1_deg	9.494
r_lrange_it	7.412
r_scangle_it	4.307
r_mcangle_it	4.3
r_scbond_it	2.981
r_mcbond_it	2.8
r_angle_refined_deg	2.285
r_nbtor_refined	0.281
r_nbd_refined	0.186
r_chiral_restr	0.176
r_symmetry_nbd_refined	0.16
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2169
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	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.